Home
Trees
Indices
Help
[
hide private
]
[
frames
] |
no frames
]
Identifier Index
[
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W X Y Z
_
]
A
add_enzymes_to_reactions()
(in
SBML_MCA.misc
)
ast_code_to_string()
(in
SBML_MCA.misc
)
ast_to_string_libsbml()
(in
SBML_MCA.misc
)
assignment_rules
(in
Model
)
ast_to_string()
(in
SBML_MCA.misc
)
C
check_equilibrium_constants()
(in
Thermodynamics
)
CompleteRandomOrder
(in
SBML_MCA.Kineticizer
)
CriticalError
(in
SBML_MCA.Errors
)
check_flux_signs()
(in
Thermodynamics
)
compute_assignment_rules()
(in
Simulator
)
check_steady_state()
(in
Thermodynamics
)
ConvenienceKinetics
(in
SBML_MCA.Kineticizer
)
D
dS_dt()
(in
Simulator
)
E
enzyme_positions
(in
Model
)
Errors
(in
SBML_MCA
)
external_species_concentrations
(in
Model
)
F
find_steady_state_flux()
(in
Thermodynamics
)
flux()
(in
Simulator
)
G
get_2nd_conc_resp()
(in
MCA
)
get_initial_conc()
(in
Model
)
get_species()
(in
Model
)
get_2nd_custom_conc_resp()
(in
MCA
)
get_jacobian()
(in
MCA
)
get_species_ids()
(in
Model
)
get_2nd_custom_flux_resp()
(in
MCA
)
get_metabolite_elasticities()
(in
MCA
)
get_species_initial_amounts()
(in
Model
)
get_2nd_custom_resp()
(in
MCA
)
get_model_id()
(in
Model
)
get_species_initial_concentrations()
(in
Model
)
get_2nd_elasticities()
(in
MCA
)
get_model_name()
(in
Model
)
get_species_names()
(in
Model
)
get_2nd_flux_resp()
(in
MCA
)
get_not_constant_species()
(in
SBML_MCA.misc
)
get_species_wo_enzymes()
(in
SBML_MCA.misc
)
get_conc_cc()
(in
MCA
)
get_not_enzyme_positions()
(in
SBML_MCA.misc
)
get_spectral_conc_cc()
(in
MCA
)
get_conc_resp()
(in
MCA
)
get_parameter_elasticities()
(in
MCA
)
get_spectral_conc_resp()
(in
MCA
)
get_custom_conc_resp()
(in
MCA
)
get_parameter_name()
(in
SBML_MCA.misc
)
get_spectral_flux_cc()
(in
MCA
)
get_custom_flux_resp()
(in
MCA
)
get_parameter_names()
(in
Model
)
get_spectral_flux_resp()
(in
MCA
)
get_delta_parameters()
(in
Model
)
get_parameter_value()
(in
SBML_MCA.misc
)
get_stability()
(in
MCA
)
get_elasticities()
(in
MCA
)
get_parameter_values()
(in
Model
)
get_steady_state()
(in
Simulator
)
get_elasticities_symbolic()
(in
MCA
)
get_reaction_ids()
(in
Model
)
get_steady_state_flux()
(in
Simulator
)
get_enzyme_catalysed_reactions()
(in
SBML_MCA.misc
)
get_reaction_kinetics()
(in
Model
)
get_time_varying_conc_rc()
(in
MCA
)
get_enzyme_for_reaction()
(in
SBML_MCA.misc
)
get_reaction_modifiers()
(in
Model
)
get_time_varying_conc_rc_numerical()
(in
MCA
)
get_enzymes()
(in
SBML_MCA.misc
)
get_reaction_names()
(in
Model
)
get_time_varying_flux_rc()
(in
MCA
)
get_flux_cc()
(in
MCA
)
get_reaction_products()
(in
Model
)
get_time_varying_rc_web_if()
(in
MCA
)
get_flux_resp()
(in
MCA
)
get_reaction_substrates()
(in
Model
)
get_formula()
(in
SBML_MCA.misc
)
get_rule_ids()
(in
Model
)
I
integrate()
(in
Simulator
)
is_enzyme()
(in
SBML_MCA.misc
)
is_species_not_constant()
(in
Model
)
integrate_return_dict()
(in
Simulator
)
is_species_changed_by_rule()
(in
Model
)
integrate_with_constant_species()
(in
Simulator
)
is_species_constant()
(in
Model
)
K
kinetic_laws
(in
Model
)
Kineticizer
(in
SBML_MCA
)
Kineticizer
(in
SBML_MCA.Kineticizer
)
M
make_unique_local_parameters()
(in
SBML_MCA.misc
)
MAX_MODEL_SIZE
(in
SBML_MCA.Model
)
misc
(in
SBML_MCA
)
MassAction
(in
SBML_MCA.Kineticizer
)
MCA
(in
SBML_MCA
)
Model
(in
SBML_MCA
)
matrix2string()
(in
SBML_MCA.misc
)
MCA
(in
SBML_MCA.MCA
)
Model
(in
SBML_MCA.Model
)
matrix2tensor()
(in
SBML_MCA.misc
)
MIN_VALUE_NORM
(in
MCA
)
myeval()
(in
SBML_MCA.Kineticizer
)
N
N
(in
Model
)
NoncriticalError
(in
SBML_MCA.Errors
)
nullspace()
(in
SBML_MCA.misc
)
N_partitioned
(in
Model
)
not_enzyme_positions
(in
Model
)
O
ode_variables
(in
Model
)
odeint_wrapper()
(in
Simulator
)
P
parameter_ids
(in
Model
)
plot_time_varying_coefficients()
(in
MCA
)
parse_input_file()
(in
SBML_MCA.Kineticizer
)
plot_timecourse()
(in
Simulator
)
R
rate_rules
(in
Model
)
replacements
(in
Model
)
reaction_ids
(in
Model
)
run_test()
(in
SBMLTestSuite
)
S
SBML_MCA
sbo_type2id
(in
SBML_MCA.Model
)
Simulator
(in
SBML_MCA.Simulator
)
SBMLTestSuite
(in
SBML_MCA
)
set_initial_conc()
(in
Model
)
solve_steady_state()
(in
Simulator
)
SBMLTestSuite
(in
SBML_MCA.SBMLTestSuite
)
set_parameter_value()
(in
SBML_MCA.misc
)
species_2_position
(in
Model
)
SBMLValidator
(in
SBML_MCA
)
set_parameter_values()
(in
Model
)
species_ids
(in
Model
)
SBMLValidator
(in
SBML_MCA.SBMLValidator
)
Simulator
(in
SBML_MCA
)
species_volume_prefactor
(in
Model
)
T
Thermodynamics
(in
SBML_MCA
)
Thermodynamics
(in
SBML_MCA.Thermodynamics
)
TIME_VARIABLE
(in
SBML_MCA.Model
)
V
validate()
(in
SBMLValidator
)
_
__init__()
(in
Kineticizer
)
_check_initial_conditions()
(in
SBMLValidator
)
_get_value_dict()
(in
MCA
)
__init__()
(in
MCA
)
_check_model_size()
(in
SBMLValidator
)
_maximal_model_size
(in
SBMLValidator
)
__init__()
(in
Model
)
_check_not_supported()
(in
Model
)
_normalize_coefficients()
(in
MCA
)
__init__()
(in
SBMLTestSuite
)
_check_not_supported_sbml_mca()
(in
SBMLValidator
)
_normalize_time_varying_coeff()
(in
MCA
)
__init__()
(in
SBMLValidator
)
_compare_results()
(in
SBMLTestSuite
)
_pack_parameters()
(in
CompleteRandomOrder
)
__init__()
(in
Simulator
)
_compute_2nd_resp()
(in
MCA
)
_pack_parameters()
(in
Kineticizer
)
__init__()
(in
Thermodynamics
)
_evaluate_initial_assignments()
(in
Model
)
_pack_parameters()
(in
MassAction
)
__package__
(in
SBML_MCA.Errors
)
_find_parameters()
(in
CompleteRandomOrder
)
_plot_simulation()
(in
SBMLTestSuite
)
__package__
(in
SBML_MCA.Kineticizer
)
_find_parameters()
(in
Kineticizer
)
_print()
(in
SBMLTestSuite
)
__package__
(in
SBML_MCA.MCA
)
_find_parameters()
(in
MassAction
)
_read_results()
(in
SBMLTestSuite
)
__package__
(in
SBML_MCA.Model
)
_generate_file_path()
(in
SBMLTestSuite
)
_read_settings()
(in
SBMLTestSuite
)
__package__
(in
SBML_MCA.SBMLTestSuite
)
_get_2nd_elasticity()
(in
MCA
)
_replace_flux_symbols()
(in
Model
)
__package__
(in
SBML_MCA.SBMLValidator
)
_get_elasticity()
(in
MCA
)
_run_single_test()
(in
SBMLTestSuite
)
__package__
(in
SBML_MCA.Simulator
)
_get_enzyme()
(in
Kineticizer
)
_set_enzyme_concentrations()
(in
Kineticizer
)
__package__
(in
SBML_MCA.Thermodynamics
)
_get_formula_factors()
(in
CompleteRandomOrder
)
_set_external_metabolite_conc()
(in
Kineticizer
)
__package__
(in
SBML_MCA
)
_get_formula_factors()
(in
ConvenienceKinetics
)
_simulate()
(in
SBMLTestSuite
)
__package__
(in
SBML_MCA.misc
)
_get_kinetic_laws()
(in
Model
)
_SMALL_FACTOR
(in
MCA
)
_accepted_errors
(in
SBMLTestSuite
)
_get_libsbml_errors()
(in
SBMLValidator
)
_test_thermodynamics()
(in
Kineticizer
)
_assign_kinetic()
(in
CompleteRandomOrder
)
_get_standard_kms()
(in
Kineticizer
)
_TRESHOLD
(in
SBMLTestSuite
)
_assign_kinetic()
(in
Kineticizer
)
_get_stoich_mat()
(in
Thermodynamics
)
_assign_kinetic()
(in
MassAction
)
_get_stoichiometry()
(in
Kineticizer
)
Home
Trees
Indices
Help
Generated by Epydoc 3.0.1 on Mon Apr 24 21:05:11 2017
http://epydoc.sourceforge.net


Components of an RL-ready model
The Reinforcement Learning (RL) experiment is a special type of AnyLogic experiment for allowing RL-ready AnyLogic models to be used on specific RL platforms. The experiment provides a platform-agnostic framework for declaring the necessary components in an RL training setup.
This experiment type is available in all three editions of AnyLogic; for PLE, limitations still apply in the exported model.
Unlike other experiments, the RL experiment cannot be directly executed by end-users within AnyLogic. This is because AnyLogic does not have any embedded RL algorithms. Thus, it can only be directly executed by compatible platforms (e.g., alpyne, Pathmind, or Microsoft Bonsai).
From your perspective (as a modeler), the purpose of this experiment type is a framework for information and thus there is no user interface - you simply fill out the fields of the experiment according to your specifications.
Filling out the RL experiment
Before using a model in Alpyne, the following needs to be decided upon and implemented:
- Configuration
This is a set of data fields which define the starting conditions of each simulation run.
It achieves similar behavior to typical AnyLogic parameters, however it is a layer ontop of them. This means you can choose which parameters you’d like to expose to the exported model (similar to how Cloud inputs work).
In the “Configuration” section of the RL experiment, you define the various names and types in the table. The code field following it is where you apply the values passed from your Python environment to your model.
Any parameters not overridden in the code field will be set to their model-default values.
Warning: This code field gets called near the very beginning of the model creation process, only after the default parameter values have been set. Therefore, you should only assign values and not try to access populations or call functions (including parameter-based ones, such as
set_parameter(...)
).
- Observation
This is a set of data fields which define the current state of your simulation run, at the point the observation is taken.
It is defined in the “Observation” section of the RL experiment, where you set the names and types in the table. The code field is where you set the value of fields with the relevant values in the model.
- Action
This is a set of data fields which define what sort of dynamic interaction can occur.
It is defined in the “Action” section of the RL experiment. You set the names and types in the table. The values will be sent from your Python code to the model, where the code field will take the values and apply them to the simulation model.
- Terminal/Stopping conditions
This is how you wish to define when the simulation should be stopped or in a terminal state. This could be as the result of an improper sequence of actions putting the model in a failing state or simply a temporal end point.
You can set the start/stop time and date in the “Model time” section of the RL experiment. The “Observation” section also has a field that expects a boolean value. If the Java keyword “true” is passed, this will mark the simulation as terminal.
- Randomness
Similar to other AnyLogic experiments, you can define whether the simulation should be executed with a fixed or random engine seed.
This is defined in the “Randomness” section of the RL experiment.
Note
Both the start/stop time/date and engine seed can be overridden within Alpyne (i.e., post-exporting the model).
About the takeAction
method
As the name suggests, the takeAction
method should be called in your model when it’s desired for an action should be taken. In other words, it should be called at certain “decision points” that you want some action to be delegated to the RL algorithm. Generally speaking, these points can be event-based or time-based.
For an example, say you have a model of a bank and your RL algorithm will be trained to minimize queue times by selecting which queue an arriving customer should wait in. In this case, you might call takeAction
in a relevant callback field corresponding to when a new customer arrives to the bank.(e.g., the On exit
field of a Source block).
If instead your RL algorithm is trained to maximize employee happiness by determining every hour who should go on a break, the takeAction
may be placed in a recurring Event object.
This method belongs to the class for the RL experiment and takes any agent as an argument. Provided that you are calling the method from inside an agent (most cases), you can use the Java keyword this
to refer to the current agent. Thus, it can be called by having the following line:
ExperimentReinforcementLearning.takeAction(this);
Alternatively, you can replace “ExperimentReinforcementLearning” with the name of your created RL experiment.
Warning
If the takeAction
method is called and the model is running in a user-environment (i.e., not via Alpyne, Bonsai, or Pathmind), a model error will be thrown! If you only plan on running the model in an available platform (i.e., Alpyne, Bonsai, or Pathmind), there’s no issue. However, if you want to run the model without needing to manually toggle this line of code, see the next section.
About the optional “mode” parameter
For most AnyLogic experiments, the same base model can be used without any extra, required modification. For example, you can run a Simulation or Monte Carlo experiment without needing to edit the model.
In contrast, the takeAction
method - which is needed to trigger a step, as part of setting up your model for RL training - will throw a model error if it’s called while the model is in a user-based environment.
If you plan to have the model run for both RL training purposes and for “traditional” experiments, it’s impractical to require manual editing. Fortunately, there’s a simple solution: create a parameter on your top-level agent that designates the model’s desired execution mode. If this is a binary choice, this could be a boolean (e.g., “inRLTraining”). If you plan to have multiple execution modes (e.g., user controlled, heuristic controlled, RL training, RL testing), you could use an integer and the built-in Value Editor to describe what concepts the values correspond to.
After adding the parameter, you’ll need to refactor your model slightly to make use of it. For example, if your “mode” parameter is a simple boolean with the name “inRLTraining”, the code for taking an action may look like:
if (inRLTraining) ExperimentReinforcementLearning.takeAction(this);
Tip
Add a line in the Configuration section of the RL experiment to set the mode parameter to the value corresponding to calling takeAction
. This way, you can be sure the method will be called, regardless of what the parameter’s default value is set to!


Gecode::Reflection::VarMapIter Class Reference
[Reflection API]
Detailed Description
Iterating a variable map.The variable map is filled dynamically while iterating over the actors of a space. The iterator will signal that it is done when all currently known variables have been iterated, but it will later become available again once new variables are encountered.
Definition at line 160 of file var-map.icc.
Public Member Functions | |
| VarMapIter (VarMap &m) | |
| Construct iterator for variable map m. | |
| bool | operator() (void) const |
| Test whether iterator still has variables or is done. | |
| VarSpec & | spec (void) const |
| Return variable specification for current iterator position. | |
| VarImpBase * | varImpBase (void) const |
| Return variable implementation for current iterator position. | |
| Var | var (void) const |
| Return variable for current iterator position. | |
| void | operator++ (void) |
| Move iterator to next variable. |
Constructor & Destructor Documentation
| Gecode::Reflection::VarMapIter::VarMapIter | ( | VarMap & | m | ) |
Member Function Documentation
| bool Gecode::Reflection::VarMapIter::operator() | ( | void | ) | const |
| VarSpec & Gecode::Reflection::VarMapIter::spec | ( | void | ) | const |
Return variable specification for current iterator position.
Definition at line 254 of file var-map.cc.
| VarImpBase * Gecode::Reflection::VarMapIter::varImpBase | ( | void | ) | const |
Return variable implementation for current iterator position.
Definition at line 257 of file var-map.cc.
| Var Gecode::Reflection::VarMapIter::var | ( | void | ) | const |
| void Gecode::Reflection::VarMapIter::operator++ | ( | void | ) |
The documentation for this class was generated from the following files:
- gecode/kernel/var-map.icc (Revision: 7297)
- gecode/kernel/var-map.cc (Revision: 7296)


Not your average Joe: Talamo edges closer to milestone
by Edited Del Mar Thoroughbred Club NotesJockey Joe Talamo, two shy of his 2,000th career victory, rode four mounts on Saturday in quest of the milestone.
Records show Talamo, 29, won No. 1,000 on April 4, 2012 in the fourth race at Santa Anita aboard Splendid Fortune, an Arnold Zetcher homebred trained by Bob Baffert. The 2-5 favorite won by seven lengths. Talamo had been in California for five years, arriving in 2007 as a 17-year-old apprentice after becoming the first “bug boy” to win a riding title at the Fair Grounds in New Orleans.
A lot has changed for Talamo personally, and Southern California racing, since No. 1,000.
He took a day off from racing during the 2015 Bing Crosby meeting to marry Elizabeth Ellis, daughter of trainer Ron Ellis, in a San Diego ceremony. An anniversary looms for the couple, who now have two sons.
And it’s no secret Southern California racing has downsized since Talamo hit four figures in victories.
“We used to win 180 to a couple hundred races a year. This year we’ve won like 70,” Talamo’s agent, Scott McClellan, said Saturday morning. “We’ve ridden around 500 horses, we used to ride 1,200. That’s the difference in lack of racing and lack of horses. We’re riding two or three a day when we used to ride seven or eight.”
The Equibase statistics bear it out. In 2012, Talamo had 208 wins from 1,256 mounts. This year the numbers are 72 wins from 496 mounts.
And approaching a milestone adds pressure.
“When I told him he was 20 out, he said ‘I wish you wouldn’t have told me, now it will take forever,” McClellan said. “We got to within six, but then the last four have taken awhile.
“We know it’s going to happen. Four of his last six have been seconds and they all looked at one time like they might win. We’ll see. We’re just hoping to get it over with, but they don’t come easy.”
Talamo’s mounts on Saturday were: Rocky Tough (2nd race), Tequila Joe (5th race), Paige Anne (6th race), and Courteous (7th race).
**Editor's Note: A check of the Equibase charts from Saturday revealed that Talamo finished second on all four mounts that he had.


{% extends "layouts/base-fullscreen.html" %} {% load static %} {% block title %} Error 404 - Page Not Found {% endblock %} {% block body_class %} login-page {% endblock body_class %} {% block stylesheets %}{% endblock stylesheets %} {% block content %}
This feature is unavailable in your region.
You can provide your input/idea to before it arrives.
Please contact {{ PRODUCT_NAME }} Support Team if you need further help.


public class Page
extends java.lang.Object
| Modifier and Type | Class and Description |
|---|---|
class |
Page.Annotation |
class |
Page.Finder |
| Constructor and Description |
|---|
Page() |
| Modifier and Type | Method and Description |
|---|---|
boolean |
AddAnnot(long ref) |
boolean |
AddAnnotAttachment(java.lang.String path,
int icon,
float[] rect)
add a file as an attachment to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license, and Document.SetCache invoked. |
boolean |
AddAnnotBitmap(Document.DocImage image,
float[] rect)
add a bitmap object as an annotation to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license, and Document.SetCache() invoked. |
boolean |
AddAnnotEditbox(float[] rect,
int line_clr,
float line_w,
int fill_clr,
float tsize,
int text_clr)
add an edit-box on page.
the font of edit box is set by Global.setTextFont in Global.Init(). this can be invoked after ObjsStart or Render or RenderToBmp. this method require premium license. |
boolean |
AddAnnotEditbox(Matrix mat,
float[] rect,
int line_clr,
float line_w,
int fill_clr,
int text_clr,
float tsize)
add an edit-box on page.
the font of edit box is set by Global.setTextFont in Global.Init(). this can be invoked after ObjsStart or Render or RenderToBmp. this method require premium license. |
boolean |
AddAnnotEllipse(float[] rect,
float width,
int color,
int fill_color)
add ellipse to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotEllipse(Matrix mat,
float[] rect,
float width,
int color,
int fill_color)
add ellipse to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotGlyph(Matrix mat,
Path path,
int color,
boolean winding)
add a user-defined glyph to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotGoto(float[] rect,
int pageno,
float top)
add goto-page link to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotHWriting(Matrix mat,
HWriting hwriting,
float orgx,
float orgy)
add hand-writing to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotInk(Ink ink)
add hand-writing to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotInk(Matrix mat,
Ink ink,
float orgx,
float orgy)
add hand-writing to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotLine(float[] pt1,
float[] pt2,
int style1,
int style2,
float width,
int color,
int icolor)
add line to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotLine(Matrix mat,
float[] pt1,
float[] pt2,
int style1,
int style2,
float width,
int color,
int fill_color)
add line to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotMarkup(int cindex1,
int cindex2,
int type)
add a text-markup annotation to page.
you should re-render page to display modified data. this can be only invoked after ObjsStart. this method require professional or premium license |
boolean |
AddAnnotMarkup(Matrix mat,
float[] rects,
int type)
add a text-markup annotation to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotPolygon(Path path,
int color,
int fill_color,
float width)
add polygon to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotPolyline(Path path,
int style1,
int style2,
int color,
int fill_color,
float width)
add polyline to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotPopup(Page.Annotation parent,
float[] rect,
boolean open) |
boolean |
AddAnnotRect(float[] rect,
float width,
int color,
int fill_color)
add rectangle to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotRect(Matrix mat,
float[] rect,
float width,
int color,
int fill_color)
add rectangle to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotRichMedia(java.lang.String path_player,
java.lang.String path_content,
int type,
Document.DocImage image,
float[] rect)
add a RichMedia annotation to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license, and Document.SetCache invoked. |
boolean |
AddAnnotStamp(float[] rect,
int icon)
add an Rubber Stamp to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotText(float[] pt)
add a sticky text annotation to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddAnnotURI(float[] rect,
java.lang.String uri)
add URL link to page.
you should re-render page to display modified data. this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
boolean |
AddContent(PageContent content,
boolean flush)
add content stream to this page.
a premium license is required for this method. |
ResFont |
AddResFont(Document.DocFont font)
add a font as resource of this page.
a premium license is required for this method. |
ResForm |
AddResForm(Document.DocForm form)
add Form as resource of this page.
a premium license is required for this method. |
ResGState |
AddResGState(Document.DocGState gstate)
add GraphicState as resource of this page.
a premium license is required for this method. |
ResImage |
AddResImage(Document.DocImage image)
add an image as resource of this page.
a premium license is required for this method. |
Ref |
Advance_GetRef()
advanced function to get reference of Page object.
this method require premium license. |
void |
Advance_Reload()
advanced function to reload page object, after advanced methods update Page object data.
all annotations return from Page.GetAnnot() or Page.GetAnnotFromPoint() shall not available. |
void |
Close()
Close page object and free memory.
|
boolean |
CopyAnnot(Page.Annotation annot,
float[] rect)
clone an annotation object to this page.
this method need a professional or premium license. |
Page.Finder |
FindOpen(java.lang.String str,
boolean match_case,
boolean whole_word)
create a find session.
|
boolean |
FlatAnnots()
remove all annotations and display it as normal content on page.
this method require premium license. |
Page.Annotation |
GetAnnot(int index)
get annotations by index.
this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
Page.Annotation |
GetAnnotByName(java.lang.String name)
get annotation by name.
this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
int |
GetAnnotCount()
get annotations count in this page.
this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
Page.Annotation |
GetAnnotFromPoint(float x,
float y)
get annotation by PDF point.
this can be invoked after ObjsStart or Render or RenderToBmp. this method require professional or premium license |
float[] |
GetCropBox()
get rotated CropBox, this method need an any type of license.
|
float[] |
GetMediaBox()
get rotated MediaBox, this method need an any type of license.
|
int |
GetRotate()
get rotate degree for page, example: 0 or 90
|
int |
ObjsAlignWord(int from,
int dir)
get index aligned by word.
|
int |
ObjsGetCharCount()
get chars count in this page.
|
java.lang.String |
ObjsGetCharFontName(int index)
get char's font name.
|
int |
ObjsGetCharIndex(float[] pt)
get char index nearest to point
|
void |
ObjsGetCharRect(int index,
float[] vals)
get char's box in PDF coordinate system, this can be invoked after ObjsStart
|
java.lang.String |
ObjsGetString(int from,
int to)
get string from range.
|
void |
ObjsStart()
get text objects to memory.
a standard license is required for this method |
boolean |
Reflow(DIB dib,
float orgx,
float orgy)
Reflow to dib.
this method require professional or premium license |
int |
ReflowGetCharColor(int iparagraph,
int ichar)
get char's fill color for display.
this method require professional or premium license |
int |
ReflowGetCharCount(int iparagraph)
get one paragraph's char count.
this method require professional or premium license |
java.lang.String |
ReflowGetCharFont(int iparagraph,
int ichar)
get char's font name.
this method require professional or premium license |
float |
ReflowGetCharHeight(int iparagraph,
int ichar)
get char's font height.
this method require professional or premium license |
void |
ReflowGetCharRect(int iparagraph,
int ichar,
float[] rect)
get char's bound box.
this method require professional or premium license |
int |
ReflowGetCharUnicode(int iparagraph,
int ichar)
get char's unicode value.
this method require professional or premium license |
float |
ReflowGetCharWidth(int iparagraph,
int ichar)
get char's font width.
this method require professional or premium license |
int |
ReflowGetParaCount()
get reflow paragraph count.
this method require professional or premium license |
java.lang.String |
ReflowGetText(int iparagraph1,
int ichar1,
int iparagraph2,
int ichar2)
get text from range.
this method require professional or premium license |
float |
ReflowStart(float width,
float scale,
boolean enable_images)
Start Reflow.
this method require professional or premium license |
boolean |
ReflowToBmp(Bitmap bitmap,
float orgx,
float orgy)
Reflow to Bitmap object.
this method require professional or premium license |
boolean |
Render_Normal(DIB dib,
Matrix mat)
render to page in normal quality
|
boolean |
Render(DIB dib,
Matrix mat)
render page to dib object.
|
void |
RenderCancel()
set page status to cancelled and cancel render function.
|
boolean |
RenderIsFinished()
check if page rendering is finished.
|
void |
RenderPrePare(DIB dib)
prepare to render.
|
boolean |
RenderThumb(Bitmap bmp)
render thumb image to Bitmap object.
the image always scale and displayed in center of Bitmap. |
boolean |
RenderThumbToBuf(int[] data,
int w,
int h)
render thumb image to int array object.
the image always scale and displayed in center of Bitmap. |
boolean |
RenderThumbToDIB(DIB dib) |
boolean |
RenderToBmp(Bitmap bitmap,
Matrix mat)
render page to Bitmap object directly.
|
boolean |
RenderToBuf(int[] data,
int w,
int h,
Matrix mat)
render page to int array directly.
|
public final Ref Advance_GetRef()
public final void Advance_Reload()
public final float[] GetCropBox()
public final float[] GetMediaBox()
public final boolean AddAnnot(long ref)
public final void Close()
public final void RenderPrePare(DIB dib)
dib
- DIB object to render. obtained by Global.dibGet().public final boolean Render(DIB dib, Matrix mat)
dib
- DIB object to render. obtained by Global.dibGet().mat
- Matrix object define scale, rotate, translate operations.public final boolean RenderToBmp(Bitmap bitmap, Matrix mat)
bitmap
- Bitmap object to render.mat
- Matrix object define scale, rotate, translate operations.public final boolean RenderToBuf(int[] data, int w, int h, Matrix mat)
data
- int array store as pixels, must length as w * h, each element formated as 0xAARRGGBBw
- width.h
- height.mat
- Matrix object define scale, rotate, translate operations.public final boolean Render_Normal(DIB dib, Matrix mat)
dib
- same as Render functionmat
- same as Render functionpublic final void RenderCancel()
public final boolean RenderThumb(Bitmap bmp)
bmp
- Bitmap to renderpublic final boolean RenderThumbToDIB(DIB dib)
public final boolean RenderThumbToBuf(int[] data, int w, int h)
data
- int array store as pixels, must length as w * h, each element formated as 0xAARRGGBBw
- h
- public final boolean RenderIsFinished()
public final void ObjsStart()
public final java.lang.String ObjsGetString(int from, int to)
from
- 0 based unicode index.to
- 0 based unicode index.public final int ObjsAlignWord(int from, int dir)
from
- 0 based unicode index.dir
- if dir < 0, get start index of the word. otherwise get last index of the word.public final void ObjsGetCharRect(int index, float[] vals)
index
- 0 based unicode index.vals
- return 4 elements for PDF rectangle.public java.lang.String ObjsGetCharFontName(int index)
index
- 0 based unicode index.public final int ObjsGetCharCount()
public final int ObjsGetCharIndex(float[] pt)
pt
- point as [x,y] in PDF coordinate.public Page.Finder FindOpen(java.lang.String str, boolean match_case, boolean whole_word)
str
- key string to find.match_case
- match case?whole_word
- match whole word?public final int GetRotate()
public final int GetAnnotCount()
public Page.Annotation GetAnnot(int index)
index
- 0 based index value. range:[0, GetAnnotCount()-1]public Page.Annotation GetAnnotFromPoint(float x, float y)
x
- x value in PDF coordinate system.y
- y value in PDF coordinate system.public Page.Annotation GetAnnotByName(java.lang.String name)
name
- name string in "NM" entry of annotation.public final boolean AddAnnotGoto(float[] rect, int pageno, float top)
rect
- link area rect [left, top, right, bottom] in PDF coordinate.pageno
- 0 based pageno to goto.top
- y coordinate in PDF coordinate, page.height is top of page. and 0 is bottom of page.public final boolean AddAnnotURI(float[] rect, java.lang.String uri)
rect
- link area rect [left, top, right, bottom] in PDF coordinate.uri
- url address, example: "http://www.radaee.com/en"public final boolean AddAnnotStamp(float[] rect, int icon)
rect
- icon area rect [left, top, right, bottom] in PDF coordinate.icon
- predefined value as below:public final boolean AddAnnotInk(Matrix mat, Ink ink, float orgx, float orgy)
mat
- Matrix for Render function.ink
- Ink objectorgx
- origin x coordinate in page. in DIB coordinate systemorgy
- origin y coordinate in page. in DIB coordinate systempublic final boolean AddAnnotHWriting(Matrix mat, HWriting hwriting, float orgx, float orgy)
mat
- Matrix for Render function.hwriting
- hand writing objectorgx
- origin x coordinate in page. in DIB coordinate systemorgy
- origin y coordinate in page. in DIB coordinate systempublic final boolean AddAnnotGlyph(Matrix mat, Path path, int color, boolean winding)
mat
- Matrix for Render function.path
- Path object.color
- text color, formated as 0xAARRGGBB.winding
- if true, using winding fill rule, otherwise using odd-even fill rule.public final boolean AddAnnotRect(Matrix mat, float[] rect, float width, int color, int fill_color)
mat
- Matrix for Render function.rect
- 4 elements for left, top, right, bottom in DIB coordinate systemwidth
- line widthcolor
- rectangle color, formated as 0xAARRGGBBfill_color
- fill color in rectangle, formated as 0xAARRGGBB, if alpha channel is 0, means no fill operation, otherwise alpha channel are ignored.public final boolean AddAnnotLine(Matrix mat, float[] pt1, float[] pt2, int style1, int style2, float width, int color, int fill_color)
mat
- Matrix for Render function.pt1
- start point, 2 elements for x,ypt2
- end point, 2 elements for x,ystyle1
- style for start point:style2
- style for end point, values are same as style1.width
- line width in DIB coordinatecolor
- line color. same as addAnnotRect.fill_color
- fill color. same as addAnnotRect.public final boolean AddAnnotEllipse(Matrix mat, float[] rect, float width, int color, int fill_color)
mat
- Matrix for Render function.rect
- 4 elements for left, top, right, bottom in DIB coordinate systemwidth
- line widthcolor
- ellipse color, formated as 0xAARRGGBBfill_color
- fill color in ellipse, formated as 0xAARRGGBB, if alpha channel is 0, means no fill operation, otherwise alpha channel are ignored.public final boolean AddAnnotPopup(Page.Annotation parent, float[] rect, boolean open)
public boolean AddAnnotMarkup(Matrix mat, float[] rects, int type)
mat
- Matrix for Render function.rects
- 4 * n rectangles, each 4 elements: left, top, right, bottom in DIB coordinate system. n is decided by length of array.type
- 0: Highlight, 1: Underline, 2: StrikeOut, 3: Highlight without round corner.public final boolean AddAnnotInk(Ink ink)
ink
- Ink object in PDF coordinate.public final boolean AddAnnotLine(float[] pt1, float[] pt2, int style1, int style2, float width, int color, int icolor)
pt1
- start point in PDF coordinate, 2 elements for x,ypt2
- end point in PDF coordinate, 2 elements for x,ystyle1
- style for start point:style2
- style for end point, values are same as style1.width
- line width in DIB coordinatecolor
- line color. same as addAnnotRect.icolor
- fill color, used to fill arrows of the line.public final boolean AddAnnotRect(float[] rect, float width, int color, int fill_color)
rect
- 4 elements for left, top, right, bottom in PDF coordinate systemwidth
- line width in PDF coordinate.color
- rectangle color, formated as 0xAARRGGBBfill_color
- fill color in rectangle, formated as 0xAARRGGBB, if alpha channel is 0, means no fill operation, otherwise alpha channel are ignored.public final boolean AddAnnotEllipse(float[] rect, float width, int color, int fill_color)
rect
- 4 elements for left, top, right, bottom in PDF coordinate systemwidth
- line width in PDF coordinatecolor
- ellipse color, formated as 0xAARRGGBBfill_color
- fill color in ellipse, formated as 0xAARRGGBB, if alpha channel is 0, means no fill operation, otherwise alpha channel are ignored.public final boolean AddAnnotEditbox(float[] rect, int line_clr, float line_w, int fill_clr, float tsize, int text_clr)
rect
- 4 elements: left, top, right, bottom in PDF coordinate system.line_clr
- color of border line, formated as 0xAARRGGBB.line_w
- width of border line.fill_clr
- color of background, formated as 0xAARRGGBB. AA must same to line_clr AA, or 0 means no fill color.tsize
- text size in PDF coordinate system.text_clr
- text color, formated as 0xAARRGGBB. AA must same to line_clr AApublic final boolean AddAnnotPolygon(Path path, int color, int fill_color, float width)
path
- must be a closed contour.color
- stroke color formated as 0xAARRGGBB.fill_color
- fill color, formated as 0xAARRGGBB. if AA == 0, no fill operations, otherwise alpha value is same to stroke color.width
- stroke width in PDF coordinatepublic final boolean AddAnnotPolyline(Path path, int style1, int style2, int color, int fill_color, float width)
path
- must be a set of unclosed lines. do not container any move-to operation except the first point in the path.style1
- style for start point:style2
- style for end point, values are same as style1.color
- stroke color formated as 0xAARRGGBB.fill_color
- fill color, formated as 0xAARRGGBB. if AA == 0, no fill operations, otherwise alpha value is same to stroke color.width
- stroke width in PDF coordinatepublic boolean AddAnnotMarkup(int cindex1, int cindex2, int type)
cindex1
- first char indexcindex2
- second char indextype
- type as following:public final boolean AddAnnotBitmap(Document.DocImage image, float[] rect)
image
- DocImage object return from Document.NewImage*();rect
- 4 elements: left, top, right, bottom in PDF coordinate system.public final boolean AddAnnotAttachment(java.lang.String path, int icon, float[] rect)
path
- absolute path name to the file.icon
- icon display to the page. values as:rect
- 4 elements: left, top, right, bottom in PDF coordinate system.public final boolean AddAnnotRichMedia(java.lang.String path_player, java.lang.String path_content, int type, Document.DocImage image, float[] rect)
path_player
- path-name to flash player. example: "/sdcard/VideoPlayer.swf", "/sdcard/AudioPlayer.swf"path_content
- path-name to RichMedia content. example: "/sdcard/video.mp4", "/sdcard/audio.mp3"type
- 0: Video, 1: Audio, 2: Flash, 3: 3Dimage
- DocImage object return from Document.NewImage*();rect
- 4 elements: left, top, right, bottom in PDF coordinate system.public final boolean AddAnnotText(float[] pt)
pt
- 2 elements: x, y in PDF coordinate system.public final boolean AddAnnotEditbox(Matrix mat, float[] rect, int line_clr, float line_w, int fill_clr, int text_clr, float tsize)
mat
- Matrix object that passed to Render or RenderToBmp function.rect
- 4 elements: left, top, right, bottom in PDF coordinate system.line_clr
- color of border line, formated as 0xAARRGGBB.line_w
- width of border line.fill_clr
- color of background, formated as 0xAARRGGBB. AA must same to line_clr AA, or 0 means no fill color.tsize
- text size in DIB coordinate system.text_clr
- text color, formated as 0xAARRGGBB. AA must same to line_clr AApublic final float ReflowStart(float width, float scale, boolean enable_images)
width
- input width, function calculate height.scale
- scale base to 72 DPI, 2.0 means 144 DPI. the reflowed text will displayed in scaleenable_images
- enable reflow images.public final boolean Reflow(DIB dib, float orgx, float orgy)
dib
- dib to renderorgx
- origin x coordinateorgy
- origin y coordinatepublic final boolean ReflowToBmp(Bitmap bitmap, float orgx, float orgy)
bitmap
- bitmap to refloworgx
- origin x coordinateorgy
- origin y coordinatepublic final int ReflowGetParaCount()
public final int ReflowGetCharCount(int iparagraph)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]public final float ReflowGetCharWidth(int iparagraph, int ichar)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]ichar
- char index range[0, ReflowGetCharCount()]public final float ReflowGetCharHeight(int iparagraph, int ichar)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]ichar
- char index range[0, ReflowGetCharCount()]public final int ReflowGetCharColor(int iparagraph, int ichar)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]ichar
- char index range[0, ReflowGetCharCount()]public final int ReflowGetCharUnicode(int iparagraph, int ichar)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]ichar
- char index range[0, ReflowGetCharCount()]public final java.lang.String ReflowGetCharFont(int iparagraph, int ichar)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]ichar
- char index range[0, ReflowGetCharCount()]public final void ReflowGetCharRect(int iparagraph, int ichar, float[] rect)
iparagraph
- paragraph index range[0, ReflowGetParaCount()-1]ichar
- char index range[0, ReflowGetCharCount()]rect
- output: 4 element as [left, top, right, bottom].public java.lang.String ReflowGetText(int iparagraph1, int ichar1, int iparagraph2, int ichar2)
iparagraph1
- first positionichar1
- first positioniparagraph2
- second positionichar2
- second positionpublic ResFont AddResFont(Document.DocFont font)
font
- font object created by Document.NewFontCID()public ResImage AddResImage(Document.DocImage image)
image
- image object created by Document.NewImage() or Document.NewImageJPEG()public ResGState AddResGState(Document.DocGState gstate)
gstate
- ExtGraphicState created by Document.NewGState();public ResForm AddResForm(Document.DocForm form)
form
- Form created by Document.NewForm();public boolean AddContent(PageContent content, boolean flush)
content
- PageContent object called PageContent.create().flush
- does need flush all resources?public boolean CopyAnnot(Page.Annotation annot, float[] rect)
annot
- Annotation object must be in this document..rect
- [left, top, right, bottom] in PDF coordinate.public boolean FlatAnnots()


This is my first threejs webGL test page, and also my very first HTML page.
HOME
Point cloud APP
Mesh ply APP


An excellent base from which to visit Mount Etna and Taormina, although it is subjected to ash fallout from the volcano. The marinas in Porto Nuovo on the eastern breakwater, offer the cheapest berths and good facilities. It is a fairly long walk to the centre of the town, but worth the effort to see the buildings there.
Position 37° 28'55"N, 15° 05'44"E (harbour entrance)
Porto di Catania is not well protected from the south and strong winds from this direction can cause significant swell inside the harbour. The inner harbour, called Porto Veccho, is better protected and is close to the town. There are a few yacht club berths here.
Porto di Riposto, to the north of Catania, is well protected from the south, but is more exposed to the NW.
Caito (well protected from all directions) and Ognina Porto Ulisse (exposed to the north) are to the south of the town.
Last updated August 2016.


|
MoveToCode
|
Public Member Functions | |
| void | PublishFeedback () |
| void | PublishResult () |
Public Attributes | |
| string | ActionName |
| float | TimeStep |
| ActionStates | ActionState |
Protected Member Functions | |
| abstract void | GoalHandle (Tgoal goal) |
| void | Start () |
| virtual void | Update () |
| void | GoalCallback (Tgoal actionGoal) |
| void | CancelCallback (Messages.Actionlib.GoalID actionGoalId) |
| void | PublishStatus () |
Protected Attributes | |
| Tgoal | ActionGoal |
| Tfeedback | ActionFeedback |
| Tresult | ActionResult |
|
protected |
|
protected |
|
protectedpure virtual |
| void RosSharp.RosBridgeClient.ActionServer< Tgoal, Tfeedback, Tresult >.PublishFeedback | ( | ) |
| void RosSharp.RosBridgeClient.ActionServer< Tgoal, Tfeedback, Tresult >.PublishResult | ( | ) |
|
protected |
|
protected |
|
protectedvirtual |
|
protected |
|
protected |
| string RosSharp.RosBridgeClient.ActionServer< Tgoal, Tfeedback, Tresult >.ActionName |
|
protected |
| ActionStates RosSharp.RosBridgeClient.ActionServer< Tgoal, Tfeedback, Tresult >.ActionState |
| float RosSharp.RosBridgeClient.ActionServer< Tgoal, Tfeedback, Tresult >.TimeStep |


ABOUT BESTFEST
The ultimate music festival site dedicated to providing fans with all the information and resources they need to get the most out of their festival experience!
THE STORY
I created BestFest for music festival fans just like myself. It all started when I was a sophomore in high school and I attended Coachella, my first festival ever. That weekend changed my life; I fell in love with everything about the music festival experience which led me to spend the next five years attending numerous events around the country. Flash forward to today, I'm still as (if not even more) passionate about music festivals!
my music festival experience
I figured that maybe, just maybe, sharing my own experiences could be useful to someone (even just one person) out there. So, I combined my love for music festivals and my experiences from attending them and created BestFest. My goal is to share with you everything you need to know to be prepared and ready to make the most out of your next festival! Here at BestFest, you can find content specific to individual events in addition to the latest festival news, announcements, and updates. You can also discover new music, explore the top tracks of the month, and even get pumped for you next festival by listening to lineup based playlists featuring songs by the performers you just can't wait to see!
START EXPLORING NOW
FESTIVAL GUIDE
Looking for your next festival? Find all the information you need from lineups and dates to location and ticket prices.
FESTIVAL GUIDENEWS
Read up on the latest news about festivals, lineup and tour announcements, music releases and more.
NEWSLISTEN
Check out our curated playlists. We have everything from new releases and top tracks to lineup-based playlists.
LISTEN


First name is required
Last name is required
Username is required
Password is required
A description is required
A list of points of interests is required


Java will initialize fields with known default values so any explicit initialization of those same defaults is redundant and results in a larger class file (approximately three additional bytecode instructions per field). Example:
public class C { boolean b = false; // examples of redundant initializers byte by = 0; short s = 0; char c = 0; int i = 0; long l = 0; float f = .0f; // all possible float literals doable d = 0d; // all possible double literals Object o = null; MyClass mca[] = null; int i1 = 0, ia1[] = null; class Nested { boolean b = false; } }


twelve columns
A simple, responsive, ultra lightweight grid framework designed to work on high resolution desktops, right down to mobile. Check it out on Github
twelve columns
four columns
eight columns
six columns
six columns
You can also nest columns.
six columns
six columns
twelve columns
six columns
six columns
twelve columns
And offset columns too
four columns offset by-one
four columns offset by-two
six columns offset by-three


References
commons
| summary | ||
| public abstract |
F glueWithCommas(args: ...string): string Concatanate all the arguments, comma-separated |
|
| public abstract |
F glueWithSpaces(args: ...string): string Concatanate all the arguments, space-separated |
mixins/animation
| summary | ||
| public abstract |
Take all the arguments and return an object with an animation property |
|
| public abstract |
F animationTimingFunction(args: ...string): object Take all the arguments and return an object with a animationTimingFunction property |
|
| public abstract |
F cubicBezier(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F transition(args: ...string): object Take all the arguments and return an object with a transition property |
|
| public abstract |
F transitionProperty(args: ...string): object Take all the arguments and return an object with a transitionProperty property |
|
| public abstract |
F transitionTimingFunction(args: ...string): object Take all the arguments and return an object with a transitionTimingFunction property |
mixins/background
| summary | ||
| public abstract |
F background(args: ...string): object Take all the arguments and return an object with a background property |
|
| public abstract |
F conicGradient(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F linearGradient(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F radialGradient(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F repeatingLinearGradient(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F repeatingRadialGradient(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take the argument and return a string with the appropriate syntax |
mixins/borders
| summary | ||
| public abstract |
Take all the arguments and return an object with a border property |
|
| public abstract |
F borderBottom(args: ...string): object Take all the arguments and return an object with a borderBottom property |
|
| public abstract |
F borderLeft(args: ...string): object Take all the arguments and return an object with a borderLeft property |
|
| public abstract |
F borderRadius(args: ...string): object Take all the arguments and return an object with a borderRadius property |
|
| public abstract |
F borderRight(args: ...string): object Take all the arguments and return an object with a borderRight property |
|
| public abstract |
Take all the arguments and return an object with a borderTop property |
mixins/box-model
mixins/filter
| summary | ||
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F brightness(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F dropShadow(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return an object with a filter property - returns "none" value if no argument is given |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
mixins/flex
| summary | ||
| public abstract |
Mixin to generate a flex box |
|
| public abstract |
F flexcolumn(mainAxis: string, secondaryAxis: string, wrap: string): object Mixin to generate a flex column |
|
| public abstract |
Mixin to generate a flex row |
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public abstract |
Take all the arguments and return an object with a flex property |
mixins/position
| summary | ||
| public abstract |
Mixin to generate a absolute positionned box |
|
| public abstract |
Mixin to generate a fixed positionned box |
|
| public abstract |
Mixin to generate a positionned box |
|
| public abstract |
Mixin to generate a relative positionned box |
|
| public abstract |
Mixin to generate a sticky positionned box |
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
|
| public |
|
mixins/size
| summary | ||
| public abstract |
Mixin to for maximal sizing (max-width/max-height) |
|
| public abstract |
Mixin to for minimal sizing (min-width/min-height) |
|
| public abstract |
Mixin to for sizing (width/height) |
mixins/transform
| summary | ||
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F perspective(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return an object with a transform property - returns "none" value if no argument is given |
|
| public abstract |
F transformOrigin(args: ...string): object Take all the arguments and return an object with a transformOrigin property |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F translate3d(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F translateX(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F translateY(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
F translateZ(args: ...string): string Take all the arguments and return a string with the appropriate syntax |
utils/colors
utils/important
utils/media
utils/units
| summary | ||
| public abstract |
Return the value with the Hz suffix |
|
| public abstract |
Return the value with the Q suffix |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Return the value with the cap suffix |
|
| public abstract |
Return the value with the ch suffix |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Return the value with the cm suffix |
|
| public abstract |
Return the value with the deg suffix |
|
| public abstract |
Return the value with the dpcm suffix |
|
| public abstract |
Return the value with the dpi suffix |
|
| public abstract |
Return the value with the dppx suffix |
|
| public abstract |
Return the value with the em suffix |
|
| public abstract |
Return the value with the ex suffix |
|
| public abstract |
Return the value with the fr suffix |
|
| public abstract |
Return the value with the grad suffix |
|
| public abstract |
Return the value with the ic suffix |
|
| public abstract |
Return the value with the in suffix |
|
| public abstract |
Return the value with the kHz suffix |
|
| public abstract |
Return the value with the lh suffix |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Take all the arguments and return a string with the appropriate syntax |
|
| public abstract |
Return the value with the mm suffix |
|
| public abstract |
Return the value with the ms suffix |
|
| public abstract |
Return the value with the pc suffix |
|
| public abstract |
Return the value with the percent suffix |
|
| public abstract |
Return the value with the pt suffix |
|
| public abstract |
Return the value with the px suffix |
|
| public abstract |
Return the value with the rad suffix |
|
| public abstract |
Return the value with the rem suffix |
|
| public abstract |
Return the value with the rlh suffix |
|
| public abstract |
Return the value with the s suffix |
|
| public abstract |
Return the value with the turn suffix |
|
| public abstract |
Return the value with the vb suffix |
|
| public abstract |
Return the value with the vh suffix |
|
| public abstract |
Return the value with the vi suffix |
|
| public abstract |
Return the value with the vmax suffix |
|
| public abstract |
Return the value with the vmin suffix |
|
| public abstract |
Return the value with the vw suffix |


ally.maintain.disabled
Example
Use the toggle inert
button to render all elements inert (except the buttons and what's within the blue border).
Use the add elements
button to see that the inert state is applied to dynamically added content as well.
Note that the disabled elements are visualized with reduced opacity and a red border only for this demo.


Changes the visibility of a source.
| Box Name | Type | Description |
|---|---|---|
| scene-name | String (optional) | Scene name containing the source. Leave blank for current active scene. |
| item | String | Source name |
| visible | boolean | True for visible, False for not visible or Toggle to invert current visibility status Toggle should be used only if it’s a single button command. |


Click here to go to the corresponding page for the latest version of DIALS
DIALS for Electron Diffraction¶
Introduction¶
DIALS has been successfully adapted for processing electron diffraction data from protein nanocrystals. Extensions to the software and protocols for dealing with the peculiarities of electron diffraction data are described in a publication:
Warning
This tutorial reproduces the data processing results described in that paper,
which were produced by DIALS version 1.dev.2084-g06727c3
and CCP4 version
7.0.051
. Results may differ with other versions of the software.
The commands listed here assume the use of a Bash shell on a POSIX-compliant system, so would have to be adjusted appropriately for use on other systems such as Windows.
Data¶
The data for this tutorial are available online at
. There are seven datasets from different
lysozyme nanocrystals stored as gzipped tar archives. These should be
downloaded and expanded to create seven directories containing the images,
Lys_ED_Dataset_{1..7}
. We recommend doing data processing for each dataset
in its own directory, separate from the images, for example
Lys_ED_Dataset_1-dials-proc
. When referring to the data directories in
commands listed in this tutorial, we shall use an environment variable pointing
to the parent directory. Assuming the current directory contains all of the
downloaded and unpacked dataset directories, we set that variable as follows in
a bash shell:
export DATA_PARENT=$(pwd)
Import¶
The images are in the standard miniCBF format, however the detector is unusual.
We have constructed a special dxtbx Format
class to interpret the images
properly. This is not distributed with DIALS, but can be found in a separate
repository here: https://github.com/dials/dxtbx_ED_formats.
We can make use of the dxtbx runtime plug-in system to pick the format class
up automatically by saving it in a special directory, $HOME/.dxtbx/
(for
POSIX-compliant systems). For example (may require installation of curl):
if [ ! -f ~/.dxtbx/FormatCBFMiniTimepix.py ]; then
mkdir -p ~/.dxtbx
curl -o ~/.dxtbx/FormatCBFMiniTimepix.py https://raw.githubusercontent.com/dials/dxtbx_ED_formats/master/FormatCBFMiniTimepix.py
fi
With the format class in place, we can look at images using
dials.image_viewer and import them to
create a datablock.json
. However, for reasons outlined in the paper, the
files have incomplete metadata. For successful processing, various aspects of
the experimental geometry must be described during import so they override the
dummy values supplied by the format class.
One feature that is specific to electron diffraction is the possibility of distortion of the diffraction pattern introduced by the electron microscope lens system. Previous investigation (https://doi.org/10.1107/S2059798317010348) determined that elliptical distortion affected six of the seven datasets. This distortion was constant across the affected datasets and the ellipse parameters were determined by calibration using powder ring patterns. DIALS can handle distortion in the image plane using a pair of look-up tables. To generate appropriate tables for the distortion correction required here, run the command:
dials.generate_distortion_maps Lys_ED_Dataset_2/frame_value_018.cbf mode=ellipse ellipse.phi=-21.0 \
ellipse.l1=1.0 ellipse.l2=0.956 ellipse.centre_xy=33.2475,33.2475
This will create a pair of files, dx.pickle
and dy.pickle
. Import
commands for each dataset are then described in the following subsections,
in each case assuming the directory has been changed to a specific processing
directory.
Dataset 1¶
We need to override the default oscillation width, the orientation of the rotation axis and the detector position. We will do that by creating a PHIL file with parameters for dials.import
cat << EOF >site.phil
geometry.scan.oscillation=0,0.076
geometry.goniometer.axes=-0.018138,-0.999803,0.008012
geometry.detector.hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-26.3525,30.535,-1890
}
EOF
Then we can import the dataset:
dials.import template=$DATA_PARENT/Lys_ED_Dataset_1/frame_value_###.cbf site.phil
For this dataset, tests with spot-finding indicated a tendency to pick up noise along panel edges close to the beam centre. We created a mask interactively using the image viewer and saved its definition to another PHIL file. We can recreate that file now as follows:
cat <<EOF >mask.phil
untrusted {
panel = 2
rectangle = 500 515 0 98
}
untrusted {
rectangle = 504 514 438 515
}
EOF
We can now generate the mask using the datablock.json
created earlier, then
re-import including the mask:
dials.generate_mask mask.phil datablock.json
dials.import template=$DATA_PARENT/Lys_ED_Dataset_1/frame_value_###.cbf site.phil mask=mask.pickle
Dataset 2¶
The dummy geometry is replaced, as before, using a site.phil
. However, the
parameter definitions are different this time. Also, for this and
following datasets we also need to include the look-up tables describing the
elliptical distortion that were created earlier.
cat << EOF >site.phil
geometry.scan.oscillation=0,0.1615
geometry.goniometer.axes=0.309,-0.951,0.000
geometry.detector.hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-23.21,26.29,-2055
}
lookup.dx=$DATA_PARENT/dx.pickle
lookup.dy=$DATA_PARENT/dy.pickle
EOF
dials.import template=$DATA_PARENT/Lys_ED_Dataset_2/frame_value_###.cbf site.phil
Dataset 3¶
For subsequent datasets the orientation of the rotation axis remains the same, but the oscillation widths and beam centres vary.
cat << EOF >site.phil
geometry.scan.oscillation=0,0.0344
geometry.goniometer.axes=0.309,-0.951,0.000
geometry.detector{
hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-22.05,26.47,-2055
}
}
lookup.dx=$DATA_PARENT/dx.pickle
lookup.dy=$DATA_PARENT/dy.pickle
EOF
dials.import template=$DATA_PARENT/Lys_ED_Dataset_3/frame_value_###.cbf site.phil
Dataset 4¶
cat << EOF >site.phil
geometry.scan.oscillation=0,0.0481
geometry.goniometer.axes=0.309,-0.951,0.000
geometry.detector.hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-23.485,26.45,-2055
}
lookup.dx=$DATA_PARENT/dx.pickle
lookup.dy=$DATA_PARENT/dy.pickle
EOF
dials.import template=$DATA_PARENT/Lys_ED_Dataset_4/frame_value_###.cbf site.phil
Dataset 5¶
cat << EOF >site.phil
geometry.scan.oscillation=0,0.0481
geometry.goniometer.axes=0.309,-0.951,0.000
geometry.detector.hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-22.345,26.41,-2055
}
lookup.dx=$DATA_PARENT/dx.pickle
lookup.dy=$DATA_PARENT/dy.pickle
EOF
dials.import template=$DATA_PARENT/Lys_ED_Dataset_5/frame_value_###.cbf site.phil
Dataset 6¶
cat << EOF >site.phil
geometry.scan.oscillation=0,0.0481
geometry.goniometer.axes=0.305,-0.952,-0.01
geometry.detector.hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-22.260,26.51,-2055
}
lookup.dx=$DATA_PARENT/dx.pickle
lookup.dy=$DATA_PARENT/dy.pickle
EOF
dials.import template=$DATA_PARENT/Lys_ED_Dataset_6/frame_value_###.cbf site.phil
Spot-finding settings for this weak dataset tended to pick up noise in the cross at the centre of Timepix quads. A mask was defined to blank these regions out:
cat <<EOF >mask.phil
untrusted {
panel = 0
rectangle = 222 515 255 260
}
untrusted {
panel = 0
rectangle = 256 262 74 514
}
untrusted {
panel = 2
rectangle = 256 262 0 358
}
untrusted {
panel = 2
rectangle = 207 514 256 262
}
EOF
then the mask was generated, and used during re-import of the images
dials.generate_mask mask.phil datablock.json
dials.import template=$DATA_PARENT/Lys_ED_Dataset_6/frame_value_###.cbf site.phil mask=mask.pickle
Dataset 7¶
cat << EOF >site.phil
geometry.scan.oscillation=0,0.0481
geometry.goniometer.axes=0.309,-0.951,0.000
geometry.detector.hierarchy{
fast_axis=1,0,0
slow_axis=0,-1,0
origin=-21.960,27.07,-2055
}
lookup.dx=$DATA_PARENT/dx.pickle
lookup.dy=$DATA_PARENT/dy.pickle
EOF
dials.import template=$DATA_PARENT/Lys_ED_Dataset_7/frame_value_###.cbf site.phil
Spot-finding¶
Suitable spot-finding settings were found interactively using the dials.image_viewer. The parameters used varied a little between datasets.
Dataset 1¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.833
sigma_strong = 1
global_threshold = 1
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=6 filter.d_min=2.5 filter.d_max=20 \
datablock.json find_spots.phil
Dataset 2¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.833
sigma_strong = 1
global_threshold = 1
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=6 filter.d_min=2.6 filter.d_max=25 \
datablock.json find_spots.phil
Dataset 3¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.8
sigma_strong = 2
global_threshold = 3
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=10 filter.d_min=3.0 filter.d_max=25 \
datablock.json find_spots.phil
Dataset 4¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.833
sigma_strong = 1
global_threshold = 0
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=6 filter.d_min=2.5 filter.d_max=25 \
datablock.json find_spots.phil
Dataset 5¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.833
sigma_strong = 1
global_threshold = 1
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=6 filter.d_min=2.5 filter.d_max=25 \
datablock.json find_spots.phil
Dataset 6¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.833
sigma_strong = 1
global_threshold = 1
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=8 max_spot_size=300 filter.d_min=3.0 filter.d_max=25 \
datablock.json find_spots.phil
Dataset 7¶
cat <<EOF >find_spots.phil
spotfinder {
threshold {
dispersion {
gain = 0.833
sigma_strong = 1
global_threshold = 1
}
}
}
EOF
dials.find_spots nproc=8 min_spot_size=6 filter.d_min=3.0 filter.d_max=25 \
datablock.json find_spots.phil
Indexing¶
Refinement of the experimental geometry was stabilised by fixing the detector distance, and \(\tau_2\) and \(\tau_3\) rotations. To do this, a PHIL parameter file was created in each processing directory for use in indexing and refinement steps.
cat <<EOF >refine.phil
refinement {
parameterisation {
detector {
fix_list = "Dist,Tau2,Tau3"
}
}
}
EOF
Datasets 1-5 & 7¶
An orthorhombic crystal model was determined and refined for all datasets, except dataset 6, with the following commands:
dials.index datablock.json strong.pickle refine.phil
dials.refine_bravais_settings indexed.pickle experiments.json refine.phil
dials.refine bravais_setting_5.json indexed.pickle refine.phil
Dataset 6¶
This dataset has particularly poor diffraction. We found it was necessary to fix the beam parameters, as well as provide the expected unit cell during indexing and a fairly soft restraint to stop the cell constants drifting away from these values. The unit cell restraint was set up using a file of PHIL definitions:
cat <<EOF >restraint.phil
refinement
{
parameterisation
{
crystal
{
unit_cell
{
restraints
{
tie_to_target
{
values=32.05,68.05,104.56,90,90,90
sigmas=0.05,0.05,0.05,0.05,0.05,0.05
}
}
}
}
}
}
EOF
at this stage we did not impose additional lattice symmetry, so kept the triclinic solution from indexing and refinement:
dials.index datablock.json strong.pickle refine.phil beam.fix=all restraint.phil unit_cell=32.05,68.05,104.56,90,90,90
dials.refine experiments.json indexed.pickle refine.phil restraint.phil
Static model refinement¶
For all these datasets there is significant uncertainty in the initial
experimental model. Although indexing was successful in each case, the refined
geometry shows some quite large differences compared with the initial geometry.
This is immediately obvious from viewing the refined_experiments.json
with
the dials.image_viewer. For example, here
is one image from the first dataset:
We did not allow the orientation of the rotation axis to refine, so errors in
that will have been compensated by changes in the detector orientation. The
dials.image_viewer displays the image as
seen in the laboratory frame rather than the detector frame, so the image looks
rotated. The fact that the detector “fast” and “slow” axes are no longer
aligned with the laboratory X and -Y axes would not in itself negatively affect
processing, but the fact that such large changes occurred during indexing meant
we chose to repeat this process starting from the refined geometry. This can be
done by re-importing the dataset using the refined geometry as a reference. On
re-import, the site.phil
files are no longer required, except for the
oscillation which is not taken from the reference file. The import commands
differ for each dataset as follows:
dials.import template=$DATA_PARENT/Lys_ED_Dataset_1/frame_value_###.cbf mask=mask.pickle \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.076
dials.import template=$DATA_PARENT/Lys_ED_Dataset_2/frame_value_###.cbf \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.1615 \ lookup.dx=$DATA_PARENT/dx.pickle lookup.dy=$DATA_PARENT/dy.pickle
dials.import template=$DATA_PARENT/Lys_ED_Dataset_3/frame_value_###.cbf \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.0344 \ lookup.dx=$DATA_PARENT/dx.pickle lookup.dy=$DATA_PARENT/dy.pickle
dials.import template=$DATA_PARENT/Lys_ED_Dataset_4/frame_value_###.cbf \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.0481 \ lookup.dx=$DATA_PARENT/dx.pickle lookup.dy=$DATA_PARENT/dy.pickle
dials.import template=$DATA_PARENT/Lys_ED_Dataset_5/frame_value_###.cbf \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.0481 \ lookup.dx=$DATA_PARENT/dx.pickle lookup.dy=$DATA_PARENT/dy.pickle
dials.import template=$DATA_PARENT/Lys_ED_Dataset_6/frame_value_###.cbf mask=mask.pickle \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.0481 \ lookup.dx=$DATA_PARENT/dx.pickle lookup.dy=$DATA_PARENT/dy.pickle
dials.import template=$DATA_PARENT/Lys_ED_Dataset_7/frame_value_###.cbf \ reference_geometry=refined_experiments.json geometry.scan.oscillation=0,0.0481 \ lookup.dx=$DATA_PARENT/dx.pickle lookup.dy=$DATA_PARENT/dy.pickle
After re-importing with refined geometry, indexing and refinement of an orthorhombic solution was done as before.
Datasets 1-5 & 7¶
dials.index datablock.json strong.pickle refine.phil
dials.refine_bravais_settings indexed.pickle experiments.json refine.phil
dials.refine bravais_setting_5.json indexed.pickle refine.phil \
output.experiments=static.json output.reflections=static.pickle
Dataset 6¶
Starting from the refined geometry, it was no longer necessary to fix the beam parameters or provide the unit cell for indexing. However, the unit cell restraint was still used.
dials.index datablock.json strong.pickle refine.phil restraint.phil
dials.refine_bravais_settings experiments.json indexed.pickle refine.phil
dials.refine bravais_setting_5.json indexed.pickle refine.phil restraint.phil \
output.experiments=static.json output.reflections=static.pickle
Scan-varying refinement¶
Appropriate parameterisations for scan-varying refinement were determined as described in the publication.
 After integration MTZs were exported for downstream processing with CCP4.
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.0 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_1.mtz
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.3 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_2.mtz
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.3 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_3.mtz
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.2 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_4.mtz
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.2 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_5.mtz
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.5 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_6.mtz
dials.integrate varying.json varying.pickle nproc=8 prediction.d_min=2.5 dials.export integrated_experiments.json integrated.pickle mtz.hklout=integrated_7.mtz
Scaling and merging¶
The following commands assume the exported MTZs have been copied into a new directory together. Resolution limits were determined for each dataset individually, as described in the publication. These limits were then applied to the unscaled MTZs, while reindexing them to obtain the correct space group, \(P 2_1 2_1 2\):
declare -A RES
RES[1]=2.0
RES[2]=2.89
RES[3]=2.85
RES[4]=2.77
RES[5]=2.64
RES[6]=3.20
RES[7]=3.0
for i in {1..7}
do
pointless hklin integrated_$i.mtz \
hklout sorted_$i.mtz > pointless_reindex_$i.log <<+
RESOLUTION HIGH ${RES[$i]}
REINDEX L,-K,H
SPACEGROUP 18
+
done
The reindexed MTZs were combined and then scaled together with AIMLESS, setting an overall resolution limit of \(2.1 \unicode{x212B}\):
pointless hklin sorted_1.mtz \
hklin sorted_2.mtz \
hklin sorted_3.mtz \
hklin sorted_4.mtz \
hklin sorted_5.mtz \
hklin sorted_6.mtz \
hklin sorted_7.mtz \
hklout combined.mtz > pointless_combine.log <<+
COPY
TOLERANCE 4
ALLOW OUTOFSEQUENCEFILES
+
aimless hklin combined.mtz hklout scaled.mtz > aimless.log <<+
resolution low 60 high 2.1
+
The scaled, merged MTZ is now ready for structure solution by molecular replacement.


Title: Pakistan Cotton Survey 2013, Round 1.2 doi:10.7910/DVN/QIUHRO The Pakistan Cotton Survey 2013, Round 1.2 dataset is sample survey output produced by a research study examining the efficiency of markets for cotton seeds in Pakistan conducted by the International Food Policy Research Institute (IFPRI) and implemented by Innovative Development Studies (IDS). The data was collected from September 2013 to November 2013. These data is part of a series of other Cotton20 survey rounds conducted between 2013 - 2015. More information relating to these data and other related documentation can be found at https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/QIUHRO The following documentation is provided alongside the tabular (.tab) format datasets Table of contents - this list provides a short description of all the datasets and accompanying documentation contained in the dataset. Two codebooks - Data codebook defining variables present in the datasets and Questionnaire level codebook Questionnaires used in the collection of the data. Missing documentation Summary or description of methodologies used Statistical scripts and other analysis pipelines used The data was collected was on the input use and pesticide poisoning symptoms up to the first picking of cotton. Its purpose was to examine the efficiency of markets for cotton seed in Pakistan with particular emphasis on the market for genetically modified cotton seed embodying insect-resistance traits from the soil bacterium Bacillus thurigiensis (Bt) that have been conferred through genetic modification. Number publications have been published using or citing these data (see related publication) Since the data is part of a series of longitudinal surveys, the researchers might combine all the survey datasets and perform longitudinal analysis comparing the insecticide using and resistance, market trends and consumer habits over the given period. The Viral Epidemiology and Control Group dropbox account for archiving purposes. Kindly note that this account serves as a means for sharing data between you (researcher) and the archivist. All data/files will immediately be transferred to a secure server for processing and storage, and later archived in our data repository. Upload your datasets, codebook, data cleaning and analysis code, and other pipelines/documentation into this folder as .zip file Regards, Lillian Chizi Mwango
I am a post-doctoral research scientist at KEMRI-Wellcome Trust Research Programme (KWTRP), in Kilifi, Kenya. I joined the programme as a project assistant in November 2005 after completion of a BSc (Nursing Sciences) Degree in Moi University. My main roles were to support inpatient surveillance of respiratory syncytial virus (RSV). Since then I have been involved in a broad range of research activities, including the development of new research protocols and expansion of the inpatient surveillance to include other respiratory pathogens.
In 2008, I was awarded a Commonwealth MSc training scholarship, and completed the MSc in Public Health in Developing Countries at the London School of Hygiene and Tropical Medicine, United Kingdom in October 2009, passing with a distinction. Upon my return, I initiated epidemiological studies to investigate the transmission patterns of a range of respiratory viruses in the community settings.
These studies formed part of my Ph.D training under the supervision of Professors D. James Nokes (affiliated to KWTRP, Kilifi, Kenya and University of Warwick, UK) and Graham F. Medley (University of Warwick, UK). I successfully defended my thesis 'Transmission of Respiratory Syncytial Virus in Households: Who Acquires Infection from Whom' at the Open University, UK in August 2013.
I am currently interested in unravelling transmission dynamics of a range of respiratory viruses in Kenya and identify potential control strategies.


Sindarin is usually written using Tengwar - the letters devised by Rúmil and improved by Fëanor. Hesperides automatically displays the Sindarin words using Tengwar thanks to the Narmacil engine, by BLiZZARD. Hesperides also offers a system service to transcribe words to Tengwar.
To transcribe words using Tengwar, Hesperides needs a mode. If you don't know what that is, or if you want to transcribe non-Sindarin words, you may want to get more information about modes.
Just type your text in another application, like TextEdit, and then choose Services → Transcribe to Tengwar in the application menu (the TextEdit menu for example). This will launch Hesperides and transcribe the text.
You can also choose a mode, once Hesperides is launched, and rerun the transcription.
If you get garbage in your text editing application, you have not installed the fonts needed to make the transcription work. Hesperides uses these fonts internally, but you have to install them to make them available to other applications if you want to use the transcription service.
To install the fonts, open the Hesperides disk image (the one you downloaded when you first installed Hesperides), go into the Fonts folder, open them (using Font Book), and click on the Install Font button.


My name is Nicole and I am an aspiring web developer. I love programming and problem solving. I also like cats and taking walks outside.
I am applying to Launch Academy because I have been to two different colleges in the past year and neither provided me with the knowledge or experience I wanted. I spent a lot of time and money without working towards my goals. For me, hours of lectures don't sink in as much as hands on learning. Also, the schools I attended barely scratched the surface of web programming and taught abstract concepts in computer science and higher level programming languages.
I've developed most of my programming skills on my own, but there are some things I just can't do by myself right now. I need an extra push so I can start making it in the real world and I think Launch Academy is just the right thing.
Take a look around the rest of my resume-style website to see where I'm at.
<EMAIL_ADDRESS>1407 Peaked Hill RdBristol NH, 03222
(603)-530-2645


{{_ 'We are ready to provide you with more information, answer your questions, and create effective solutions for your recruitment needs.'}}
{{_ 'Please select the purpose of your inquiry. If you have questions, would like to request quotation, or would like to setup an appointment with one of our business managers, do not hesitate to contact us. '}}


Back to all versions
Version 7 - August/September 2017
Journeys
What we are testing
- GDPR changes
- Return journey
- Change your details journey
- Digital reminders
Email content:
Text:
You have prepaid for NHS prescriptions.
Prepayment for: Andrew McLean
Prepayment number: 123 456 789
Start date: 15 March 2017
End date: 14 June 2017
Visit https://ppc-prototype.herokuapp.com/return/return_start
if you need to change your personal details.
Visit http://bit.ly/2jPn3B1 to opt out of receiving text messages.


CCFilter returns true if the given chaincode should be included in the invocation chain when computing endorsers.
type CCFilter func(ccID string) bool
func NewChainedCCFilter(filters ...CCFilter) CCFilter
NewChainedCCFilter returns a chaincode filter that chains multiple filters together. False is returned if at least one of the filters in the chain returns false.
ClientContext contains context parameters for handler execution
type ClientContext struct { CryptoSuite core.CryptoSuite Discovery fab.DiscoveryService Selection fab.SelectionService Membership fab.ChannelMembership Transactor fab.Transactor EventService fab.EventService }
CommitTxHandler for committing transactions
type CommitTxHandler struct {
// contains filtered or unexported fields
}
func NewCommitHandler(next ...Handler) *CommitTxHandler
NewCommitHandler returns a handler that commits transaction propsal responses
func (c *CommitTxHandler) Handle(requestContext *RequestContext, clientContext *ClientContext)
Handle handles commit tx
EndorsementHandler for handling endorse transactions
type EndorsementHandler struct {
// contains filtered or unexported fields
}
func NewEndorsementHandler(next ...Handler) *EndorsementHandler
NewEndorsementHandler returns a handler that endorses a transaction proposal
func NewEndorsementHandlerWithOpts(next Handler, provider TxnHeaderOptsProvider) *EndorsementHandler
NewEndorsementHandlerWithOpts returns a handler that endorses a transaction proposal
func (e *EndorsementHandler) Handle(requestContext *RequestContext, clientContext *ClientContext)
Handle for endorsing transactions
EndorsementValidationHandler for transaction proposal response filtering
type EndorsementValidationHandler struct {
// contains filtered or unexported fields
}
func NewEndorsementValidationHandler(next ...Handler) *EndorsementValidationHandler
NewEndorsementValidationHandler returns a handler that validates an endorsement
func (f *EndorsementValidationHandler) Handle(requestContext *RequestContext, clientContext *ClientContext)
Handle for Filtering proposal response
Handler for chaining transaction executions
type Handler interface { Handle(context *RequestContext, clientContext *ClientContext) }
func NewExecuteHandler(next ...Handler) Handler
NewExecuteHandler returns execute handler with chain of SelectAndEndorseHandler, EndorsementValidationHandler, SignatureValidationHandler and CommitHandler
func NewQueryHandler(next ...Handler) Handler
NewQueryHandler returns query handler with chain of ProposalProcessorHandler, EndorsementHandler, EndorsementValidationHandler and SignatureValidationHandler
func NewSelectAndEndorseHandler(next ...Handler) Handler
NewSelectAndEndorseHandler returns a new SelectAndEndorseHandler
Opts allows the user to specify more advanced options
type Opts struct { Targets []fab.Peer // targets TargetFilter fab.TargetFilter TargetSorter fab.TargetSorter Retry retry.Opts BeforeRetry retry.BeforeRetryHandler Timeouts map[fab.TimeoutType]time.Duration ParentContext reqContext.Context //parent grpc context CCFilter CCFilter }
ProposalProcessorHandler for selecting proposal processors
type ProposalProcessorHandler struct {
// contains filtered or unexported fields
}
func NewProposalProcessorHandler(next ...Handler) *ProposalProcessorHandler
NewProposalProcessorHandler returns a handler that selects proposal processors
func (h *ProposalProcessorHandler) Handle(requestContext *RequestContext, clientContext *ClientContext)
Handle selects proposal processors
Request contains the parameters to execute transaction
type Request struct { ChaincodeID string Fcn string Args [][]byte TransientMap map[string][]byte // InvocationChain contains meta-data that's used by some Selection Service implementations // to choose endorsers that satisfy the endorsement policies of all chaincodes involved // in an invocation chain (i.e. for CC-to-CC invocations). // Each chaincode may also be associated with a set of private data collection names // which are used by some Selection Services (e.g. Fabric Selection) to exclude endorsers // that do NOT have read access to the collections. // The invoked chaincode (specified by ChaincodeID) may optionally be added to the invocation // chain along with any collections, otherwise it may be omitted. InvocationChain []*fab.ChaincodeCall }
RequestContext contains request, opts, response parameters for handler execution
type RequestContext struct { Request Request Opts Opts Response Response Error error RetryHandler retry.Handler Ctx reqContext.Context SelectionFilter selectopts.PeerFilter PeerSorter selectopts.PeerSorter }
Response contains response parameters for query and execute transaction
type Response struct { Proposal *fab.TransactionProposal Responses []*fab.TransactionProposalResponse TransactionID fab.TransactionID TxValidationCode pb.TxValidationCode ChaincodeStatus int32 Payload []byte }
SelectAndEndorseHandler selects endorsers according to the policies of the chaincodes in the provided invocation chain and then sends the proposal to those endorsers. The read/write sets from the responses are then checked to see if additional chaincodes were invoked that were not in the original invocation chain. If so, a new endorser set is computed with the additional chaincodes and (if necessary) endorsements are requested from those additional endorsers.
type SelectAndEndorseHandler struct { *EndorsementHandler // contains filtered or unexported fields }
func (e *SelectAndEndorseHandler) Handle(requestContext *RequestContext, clientContext *ClientContext)
Handle selects endorsers and sends proposals to the endorsers
SignatureValidationHandler for transaction proposal response filtering
type SignatureValidationHandler struct {
// contains filtered or unexported fields
}
func NewSignatureValidationHandler(next ...Handler) *SignatureValidationHandler
NewSignatureValidationHandler returns a handler that validates an endorsement
func (f *SignatureValidationHandler) Handle(requestContext *RequestContext, clientContext *ClientContext)
Handle for Filtering proposal response
TxnHeaderOptsProvider provides transaction header options which allow the provider to specify a custom creator and/or nonce.
type TxnHeaderOptsProvider func() []fab.TxnHeaderOpt


This is a grid editor built on VueJS to simulate something like a spreadsheet. Use Keyboard to navigate in the grid, hit ENTER or Double Click to edit a cell, ESC to cancel editing. Use Ctrl+C or Ctrl+V to Copy and Paste respectively and backspace to delete. Ctrl+Z helps you undo actions of shortcut keys


--- status: "ready" title: "Mosaic" text: "Used for featuring a set of similiar content" ---
Discover your next steps for what needs to be done once you arrive.


Penn Labs and the Undergraduate Assembly are proud to present PennMobile, the university’s official mobile app. Both organizations are dedicated to enhancing student life on campus, and PennMobile is the latest initiative to do just that.
With the new Penn Mobile App, you can access menus and dining hall hours for every dining hall at Penn, anytime.
Shopping classes? Find out where and when they're meeting with Course Search.
Find your professor's emails with Penn Directory. Faculty Search is at your fingertips.
Check out the DP, Events@Penn, Under the Button and 34th Street directly from your phone.
Don't want to trek across campus after that final? Now catch the elusive Penn Transit Shuttle with our Transit Scheduling features.
For all your emergencies...We have all the numbers you need - for when you want a safe walk home, medical help, or police support!


Returns the value of the cells in a reference.
Syntax
DEREF(reference)
Reference is the cell or cells from which you want to obtain a value. If reference is the reference of a single cell, DEREF returns the value of that cell. If reference is the reference of a range of cells, DEREF returns the array of values in those cells. If reference refers to the active sheet, it must be an absolute reference. Relative references are converted to absolute references.
Remarks
In most formulas, there is no difference between using a value and using the reference of a cell containing that value. The reference is automatically converted to the value, as necessary. For example, if cell A1 contains the value 2, then the formula =A1+1, like the formula =2+1, returns the result 3, because the reference A1 is converted to the value 2. However, in a few functions, such as the SET.NAME function, references are not automatically converted to values. Instead, those functions behave differently depending on whether an argument is a reference or a value.
Example
See the sixth example for SET.NAME.
Related Function
SET.NAME Defines a names as a value
Return to index


Guessing Game
Guessing Game - Game of pure luck
How does this game work?
Computer will choose a number between 1-100 randomly and memorize it.
You have to guess the number which computer has chosen.
The game continues until you guess the right number.
Refresh to start a new game.


London is the capital city of England. It is the most populous city in the United Kingdom, with a metropolitan area of over 13 million inhabitants.
我的第一个段落。


EIM WebMail is user friendly and has loads of new features:
- Get your<EMAIL_ADDRESS>- Enhanced Arabic Support
- Email2MMS Composer
- Advanced Mail Filters
- Vacation Auto Responder
- 50+ Skins
Browsing difficulties?
If you are experiencing a compatibility issue with your browser to access the mail, click here to access with your existing credentials.
Note: Your address book will be copied automatically within 24 hours after your first log-in.


Please feel free to ask for help in the forum
From
To
This example is using Google geocode for the autocomplete function (which might not be the best way for mobile devices) and Google Places for the results.


--- layout: post title: What it was like to attend DDD Immersion Course date: 2010-03-05 01:07:27.000000000 -07:00 type: post published: true status: publish categories: - News tags: [] meta: _gcid: '177' _gcuser: Vladimir Gitlevich content_type: story Summary: '2' _bitly_trim: http://dddcommunity.org/?p=88 _edit_last: '3109' _dependencies: s:6:"a:0:{}"; _custom_background: a:5:{s:3:"url";s:0:"";s:16:"background-color";s:0:"";s:17:"background-repeat";s:6:"repeat";s:21:"background-attachment";s:6:"scroll";s:19:"background-position";s:8:"left top";} _intro_text: default _intro_custom_banner: a:1:{s:3:"url";s:0:"";} U_S_C_message: '' author: login: Vladimir Gitlevich email<EMAIL_ADDRESS>display_name: Vladimir Gitlevich first_name: Vladimir Gitlevich last_name: '' ---
Read a series of very informative blog posts by Paul Rayner on what it was like to attend DDD Immersion Course.


Call us today or order online!
715-634-2785 or 1-800 40-FUDGE
Mail orders are shipped promptly.
home
homemade candies
olde-tyme candies
our story
special events
contact us
(
items
)
Open Shopping Cart
Proceed to checkout
Chocolate Fudge
$7.99 per pound
Add to Cart
Vanilla Fudge
$7.99 per pound
Add to Cart
Maple Fudge
$7.99 per pound
Add to Cart
Peanut Butter Fudge
$7.99 per pound
Add to Cart
Chocolate Peanut Butter Fudge
$7.99 per pound
Add to Cart
Chocolate Nut Fudge
$9.99 per pound
Add to Cart
Vanilla Nut Fudge
$9.99 per pound
Add to Cart
Maple Nut Fudge
$14.99 per pound
Add to Cart
Peanut Butter Nut Fudge
$9.99 per pound
Add to Cart
Chocolate Peanut Butter Nut Fudge
$9.99 per pound
Add to Cart
Dark Chocolate Fudge
$14.99 per pound
Add to Cart
Dark Chocolate Nut Fudge
$14.99 per pound
Add to Cart
Sea Salt Turtle Fudge
$14.99 per pound
Add to Cart
World Famous Turtles
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Chocolate Fudge Balls
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Chocolate Peanut Butter Fudge Balls
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Vanilla Fudge Balls
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Sea Salt Caramel Fudge Balls
$15.99 per pound
What's your flavor?
Milk Chocolate
Dark Chocolate
Add to Cart
Mint Balls
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Coconut Balls
$15.99 per pound
--What's your flavor?--
Toasted Coconut
Coconut Cream
Add to Cart
Oreo Cookie Delights
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Chocolate Covered Oreos
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Haystacks
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Sea Monsters
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
English Toffee
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
Add to Cart
Chocolate Pretzals
$15.99 per pound
--What's your flavor?--
Milk Chocolate
Dark Chocolate
White Chocolate
Add to Cart
Smores
$15.99 per pound
Add to Cart
Chocolate Almond Nut Clusters
$15.99 per pound
Also comes in Sugar-Free!
--What's your flavor?--
Milk Chocolate
Sugarfree Milk Chocolate
White Chocolate
Sugarfree Dark Chocolate
Add to Cart
Chocolate Pecan Nut Clusters
$15.99 per pound
Also comes in Sugar-Free!
--What's your flavor?--
Milk Chocolate
Sugarfree Milk Chocolate
Dark Chocolate
Sugarfree Dark Chocolate
Add to Cart
Chocolate Peanut Clusters
$15.99 per pound
Also comes in Sugar-Free!
--What's your flavor?--
Milk Chocolate
Sugarfree Milk Chocolate
Dark Chocolate
Sugarfree Dark Chocolate
Add to Cart
Chocolate Cashew Nut Clusters
$15.99 per pound
Also comes in Sugar-Free!
--What's your flavor?--
Milk Chocolate
Sugarfree Milk Chocolate
Dark Chocolate
Sugarfree Dark Chocolate
Add to Cart
Peanut Brittle
$8.99 per pound
Add to Cart
Cashew Brittle
$9.99 per pound
Add to Cart
Almond Bark
$8.99 per pound
Also comes in Sugar-Free!
--What's your flavor?--
Chocolate
Sugarfree Chocolate
Vanilla
Sugarfree Vanilla
Add to Cart
Nut Logs
$15.99 per pound
--What's your flavor?--
Peanut
Cashew
Add to Cart
Fudge or Caramel Sauce
$8.99 per pound
--What's your flavor?--
Fudge
Caramel
Add to Cart
×
Shopping Cart
Remove
Qty
Item Name
Cost
Subtotal


Finance Team is responsible for obtaining, maintaining, and gaining money for Magnify Wellness via creating budgets, applying for grants such as Bay Area Global Health Challenges, J.M.K Innovation, Fast Forward Accelerator Grant, and S.M.A.R.T grant. Finance Team is also responsible for collaborating with the tech and social media teams in determining prices for current and future magnify wellness merch to be put on the website.
My name is Labib Joarder and I’m currently attending the University of Washington. I joined Magnify Wellness because I am really interested in helping people my age with their mental health.
Ella is currently a student at Foothill High School in the Bay Area of California. She joined Magnify Wellness to help promote equal access to mental health resources for everyone.
My name is Autumn Tyler and I’m a sophomore in High School. I joined Magnify because I want to help my community with their mental health issues.