|
Midnight Blue Game and Engine
|
Planet metadata used as information and arguments for generating the actual biome map of a planet. Required for an entity to be treated as a planet. More...
Properties | |
| string | Name [get, set] |
| Gets or sets the name of the planet. More... | |
| int | Radius [get, set] |
| Gets or sets the radius of the planet. More... | |
| PlanetType | Type [get, set] |
| Gets or sets the type of the planet. More... | |
| float | SurfaceTemperature [get, set] |
| Gets or sets the surface temperature. More... | |
| int | Density [get, set] |
| Gets or sets the density. More... | |
| float | Habitable [get, set] |
| Gets or sets the score indicating the planets ability to support life. More... | |
| int | Carbon [get, set] |
| Gets or sets the amount of carbon on the planet. More... | |
| int | Water [get, set] |
| Gets or sets the amount of water on the planet. More... | |
| int | Gas [get, set] |
| Gets or sets the amount of gas on the planet. More... | |
| Length | StarDistance [get, set] |
| Gets or sets the distance of this planet to its star More... | |
| float | SurfaceArea [get] |
| Gets the surface area of the planet. Used mostly for information displays - not very useful for anything else. More... | |
Planet metadata used as information and arguments for generating the actual biome map of a planet. Required for an entity to be treated as a planet.
|
getset |
Gets or sets the amount of carbon on the planet.
The carbon amount.
|
getset |
Gets or sets the density.
The density.
|
getset |
Gets or sets the amount of gas on the planet.
The gas amount.
|
getset |
Gets or sets the score indicating the planets ability to support life.
The life score.
|
getset |
Gets or sets the name of the planet.
The name.
|
getset |
Gets or sets the radius of the planet.
The radius.
|
getset |
Gets or sets the distance of this planet to its star
The star distance.
|
get |
Gets the surface area of the planet. Used mostly for information displays - not very useful for anything else.
The surface area.
|
getset |
Gets or sets the surface temperature.
The surface temperature.
|
getset |
Gets or sets the type of the planet.
The type.
|
getset |
Gets or sets the amount of water on the planet.
The water amount.


Lab 1 - Intro to Bioinformatics Databases
28 Sep 20171. Lab intro
2. Answer questions about Human Hemoglobin - subunit beta
What chromosome is HBB on?
How many exons does this gene have?
Briefly describe how the gene works?
What diseases are caused by mutations in the gene?
Find a paper that describes an aspect of HBB’s function
- Go to HackMD
- Copy these questions to a new document and save as Lab1.md
- Fill in answers to each qustion
- Export as HTML
- Submit file on Canvas under Assignments
Here is a guide to composing documents using Markdown: Markdown Cheatsheet
On HackMD, you can collaborate on documents by sharing the URL. You can also download the document to your computer to save it, and re-upload it later. You can also drag images onto your document and it will upload them.
3. Exploration of NCBI
4. Begin Project 1
Lists of databases:


--- layout: post title: "Restore Finder magic to a sparsebundle directory" permalink: /posts/bundle-magic date: 2008-01-03 author: "Nic Benders" comments: false external-url: categories: ---
This is a quick fix to restore t he special behavior of a .sparsebundle directory in Finder.
While experimenting with TimeMachine’s unsupported network backup capabilities I rsync’d my host_blah.sparsebundle
from one drive to another (without using -E
, more on that later). The result was that my .sparsebundle
now appeared in the Finder just as a normal folder, instead of with a disk image icon. This also meant that I couldn’t open the image in DiskUtility any more.
The fix is to use SetFile to restore the “Bundle” attribute.
$ /Developer/Tools/SetFile -a B host_blah.sparsebundle
The first time I mounted it afterwards I had to wait for fsck_hfs to complete, since the “com.apple.diskimages.fsck” attribute had been cleared, but otherwise it’s back to it’s old self.
I also learned that in order to avoid this (and many other much nastier problems) you should use the -E
flag for rsync under Mac OS. This correctly copies over the resource forks, extended attributes and meta-data also.
(This item is probably old-hat to many Mac users, since Bundles have been in the Finder since OS 9. But it took me a couple of days of searching and experimentation, so I figure it could use some better visibility.)


Event Guest Attendance
account_circle
business
phone
add
Name
Organization
Contact Number
Date & Time


API methods related to the friends and so on of one gamer.
You may also want to subscribe to related events (see CotcSdk.GamerCommunity.OnFriendStatusChange).
◆ OnFriendStatusChange
Event triggered when someone adds this gamer as a friend or changes his friendship status.
◆ AddFriend()
Easy way to add a friend knowing his gamer ID inside the CotC community.
- Returns
- Promise resolved when the operation has completed.
- Parameters
-
| gamerId | ID of the gamer to add as a friend (fetched using ListFriends for instance). |
| notification | Optional OS notification to be sent to indicate the player that the status has changed. |
◆ ChangeRelationshipStatus()
Allows to change the relation of a friendship inside the application.
- Returns
- Promise resolved when the operation has completed.
- Parameters
-
| gamerId | ID of the gamer to change the relationship (fetched using ListFriends for instance). |
| state | The new state to set. |
| notification | Optional OS notification to be sent to indicate the player that the status has changed. |
◆ DiscardEventHandlers()
| void CotcSdk.GamerCommunity.DiscardEventHandlers |
( |
| ) |
|
Clears all event handlers subscribed, ensuring that a match object can be dismissed without causing further actions in the background.
◆ Domain()
Changes the domain affected by the next operations. You should typically use it this way: gamer.Community.Domain("private").ListFriends(...);
- Parameters
-
| domain | Domain on which to scope the next operations. |
- Returns
- This object for operation chaining.
◆ ListFriends()
Method used to retrieve the application's friends of the currently logged in profile.
- Returns
- Promise resolved when the operation has completed, with the fetched list of friends.
- Parameters
-
| filterBlacklisted | When set to true, restricts to blacklisted friends. |
◆ ListNetworkFriends()
When you have data about friends from another social network, you can post them to CotC servers using these function. This will automatically add them as a friend on CotC as they get recognized on our servers. The friends get associated to the domain of this object. Note: this function was once called PostSocialNetworkFriends but renamed due to it being misleading.
- Returns
- Promise resolved when the operation has completed. The attached value is the same list as passed, enriched with potential information about the gamer (member CotcSdk.SocialNetworkFriend.ClanInfo) for gamers who are already registered on CotC servers.
- Parameters
-
| network | The network with which these friends are associated. |
| friends | A list of data about the friends fetched on the social network. |
| automatching | If true, synchronizes the CotC friends with the list. That is, the provided social network friends become your friends on CotC as well (reported on ListFriends and such). |
◆ SendEvent()
Use this method to send a message to another user from your game.
Messages are sent to a specific user, in a specific domain. You can use domains to send messages across games (or use private for messages sent to your game only).
- Returns
- Promise resolved when the operation has completed.
- Parameters
-
| gamerId | ID of the recipient gamer. |
| eventData | JSON object representing the event to be sent. The recipient will receive it as is when subscribed to a CotcSdk.DomainEventLoop (ReceivedEvent property). If the application is not active, the message will be queued and transmitted the next time the domain event loop is started. |
| notification | Push notification to send to the recipient player if not currently active. |


I am good at resisting temptation.
I have a hard time breaking bad habits.
I am lazy.
I say inappropriate things.
I do certain things that are bad for me, if they are fun.
I refuse things that are bad for me.
I wish I had more self-discipline.
People would say that I have iron self-discipline.
Pleasure and fun sometimes keep me from getting work done.
I have trouble concentrating.
I am able to work effectively toward long-term goals.
Sometimes I can't stop myself from doing something, even if I know it is wrong.
I often act without thinking through all the alternatives.


Begin: {{selectedExperiment.startTime | date:'short'}},
End:
{{selectedExperiment.endTime | date:'short'}}
Overall duration: {{selectedExperiment.duration}}
|
Score: {{currentIterationEntries[i][j].inceptionScore | number:'1.1-3'}}
Identities: {{currentIterationEntries[i][j].generators[0].cellId}}, {{currentIterationEntries[i][j].discriminators[0].cellId}}
|
{{selectedExperiment.settings | json}}
Neighborhood: {{result.mixtureCenter}}
Score: {{result.inceptionScore[0]}} ± {{result.inceptionScore[1]}}


Spotify's Magic Leap app lets you virtually pin music on the wall
You can create separate soundscapes for all the different rooms in your home.
by Igor BonifacicBy this point, most people have used Spotify on almost every platform where it's available and there's not a lot about the experience that's surprising. So it's interesting then to see how, with the help of augmented reality startup Magic Leap, Spotify has managed to think of a new way to organize your music library. With the company's new Magic Leap app, you can pin albums, artists and tracks to specific locations in your home. In this way, you can create a different soundscape for each room.
Spotify is also the first app on Magic Leap to take advantage of the platform's Background Music Service (BMS) API, allowing you to continue listening to music even when you switch to another app. Additionally, because the headset experience is integrated with Spotify's other apps on mobile and desktop, you don't need to take off the headset to play different songs or albums.
The fact that Spotify is now available on Magic Leap's headset probably won't help the company sell more of its pricey devices, but for those who already own one, it's a nice addition.


The main goal of the Tensorpose is to generate 2D or 3D humanoid animations from a human pose estimation obtained from an image or video.
In this project we created a framework for digital puppeteering performances, using solely the performer’s bare hands. The framework uses Unity as a base, and hand information is captured using a Leap Motion device. The performer uses a gesture interaction system and precise hand movements to manipulate the puppet in a number of different manners. It is then possible for the audience to view the puppet directly on a big screen, or using virtual or augmented reality headsets, which allows rich interactions.
It is a technological platform for the exploration of content in virtual reality. The technological infrastructure used in VR Tour is based on the VR Kino+Theater platform that exploits concepts of Situated Participatory Virtual Reality and Live 3D Digital Cinema.
The Tempest is an experiment based on Shakespeare's play combining theatrical performance with live cinema using virtual reality and gaming technologies. It was produced as a proof-of-concept of the VR Kino+Theater platform.
It is a platform that integrates traditional forms of entertainment (theater and cinema), with advanced interactive media, virtual reality and gaming. In this way, it solves the scalability of audience and presentation familiarity, while providing greater flexibility for innovative alternative formats. This platform was implemented in Unity.
This project aims to study archeological artefacts through digital technology. More specifically, it focuses on 3D reconstruction and visualization of the Egypt collection of the Museu Nacional. The project was developed in Unity.
New Realities gives a glimpse of what will be possible in future applications that exploit location-based multiplayer VR experiences. It was implemented in Unity.
It is a platform for music experimentation. It is inspired by the tradition of laptop orchestras initiated at the Princeton University in 2005. The project was developed in HTML5, CSS, and Javascript.
ReactToon is an authoring tool for collaborative creation of stories for children. With a library of objects, children can manipulate scenes and characters in a multi-touch table and create a story that the imagination can think of. The 2D version was implemented in Processing(Java) and the 3D version was implemented in Panda 3D (Python).
MUAN is a Stop Motion Animation System for Education. It consists of programs to create, edit, manipulate and visualize animations. The software was conceived by ANIMA MUNDI (International Animation Festival of Brazil) and developed by the team of VISGRAF Laboratory, with the sponsorship of IBM.
The game GP Brasil is an arcade car racing game that was entirely produced based on open source software, using the GNU/Linux operating system and open libraries for manipulating graphics, sounds and physics simulation.


{{ define "title" }}
Project Lead Developer
Started the project together with Roland and Guillaume back in 2011. In mid 2013 Manjaro was still in beta stage! Now he is working with the community to build an amazing Linux distribution.
Developer
Coordinating Community Editions with a focus on Cinnamon, Deepin and i3. He is involved in our development tools, package maintaining and optimisation within our hardware projects.
Developer
He is working on libpamac, Pamac Gtk, libpamac Python bindings, and everything Gnome related.
Community Lead | Sysadmin | Developer
Part of the project since seeing its potential in 2013, now spending time on managing the community, maintaining manjaro32, cultivating wider working relationships, developing infrastructure, packaging, and trying to ensure enthusiasm doesn't overtake common sense.
Developer
Supporting the Development in multiple ways. Gnome is his daily desktop environment. Talk to him about packaging, Gnome, Budgie and GTK Themes.
DevOps | Engineer | SysAdmin
Works on Openbox, lxde, lxqt editions also maintains pacman-mirrors, manjaro-application-utility and does forum support.
Developer
Works on manjaro-architect and gnome-layout-switcher. Maintains Bspwm edition and related packages, while also lending a helping hand on the Gnome edition.
ARM Lead Developer
Works on ARM editions including tools and infrastructure.
ARM Developer
He collaborates on ARM editions, tools and infrastructure.
Web Developer
Works on the website, MS-Office-Online backend, some occasional packaging and the conceptual Just-Another-Desktop-Environment.
Developer | Speaker
Speaker at Linux Events in Germany and Austria. He also collaborates on the Cinnamon edition, and develops Manjaro backup and security solutions.
Designer | Illustrator
Joined the Manjaro artwork team with energetic and passionate involvement.
Developer
Works on Pamac-QT
Developer
Works on website, documentation and some related native apps.
Motivator
I keep the team sharp, they start working when I do.


@(habitant: Habitant)
Name:
@habitant.name
Surname:
@habitant.surname
Patronymic:
@habitant.patronymic
Birthday:
@habitant.birthday
WorkingCapacity:
@habitant.workingCapacity
Current Work:
@vac.vacancyType.name
} else {is not working
}Organization:
VacancyType:


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java.lang.Object edu.biu.scapi.interactiveMidProtocols.commitmentScheme.elGamal.CmtElGamalReceiverCore
public abstract class CmtElGamalReceiverCore
This abstract class performs all the core functionality of the receiver side of ElGamal commitment. Specific implementations can extend this class and add or override functions as necessary.
| Constructor Summary | |
|---|---|
CmtElGamalReceiverCore(Channel channel,
DlogGroup dlog,
ElGamalEnc elGamal)
Constructor that receives a connected channel (to the receiver), the DlogGroup agreed upon between them and the encryption object. |
| Method Summary | |
|---|---|
CmtElGamalCommitmentMessage |
getCommitmentPhaseValues(long id)
Return the intermediate values used during the commitment phase. |
java.lang.Object[] |
getPreProcessedValues()
Return the values used during the pre-process phase (usually upon construction). |
CmtRCommitPhaseOutput |
receiveCommitment()
Runs the commit phase of the commitment scheme. |
CmtCommitValue |
receiveDecommitment(long id)
Runs the decommit phase of the commitment scheme. |
| Methods inherited from class java.lang.Object |
|---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Methods inherited from interface edu.biu.scapi.interactiveMidProtocols.commitmentScheme.CmtReceiver |
|---|
generateBytesFromCommitValue, verifyDecommitment |
| Constructor Detail |
|---|
public CmtElGamalReceiverCore(Channel channel, DlogGroup dlog, ElGamalEnc elGamal) throws SecurityLevelException, InvalidDlogGroupException, java.lang.ClassNotFoundException, java.io.IOException, CheatAttemptException
SecurityLevelException
InvalidDlogGroupException
java.lang.ClassNotFoundException
java.io.IOException
CheatAttemptException
| Method Detail |
|---|
public CmtRCommitPhaseOutput receiveCommitment() throws java.lang.ClassNotFoundException, java.io.IOException
Pseudo code:
"WAIT for a value c
STORE c".
receiveCommitment
in interface CmtReceiver
java.lang.ClassNotFoundException
- if there was a problem during serialization mechanism.
java.io.IOException
- if there was a problem during communication phasepublic CmtCommitValue receiveDecommitment(long id) throws java.lang.ClassNotFoundException, java.io.IOException, java.lang.IllegalArgumentException
Pseudo code:
"WAIT for (r, x) from C
Let c = (h,u,v); if not of this format, output REJ
IF NOT
• u=g^r
• v = h^r * x
• x in G
OUTPUT REJ
ELSE
OUTPUT ACC and value x"
receiveDecommitment
in interface CmtReceiver
id
-
java.lang.ClassNotFoundException
- if there was a problem during serialization mechanism.
java.io.IOException
- if there was a problem during communication phase
java.lang.IllegalArgumentException
public java.lang.Object[] getPreProcessedValues()
CmtReceiver
getPreProcessedValues
in interface CmtReceiver
public CmtElGamalCommitmentMessage getCommitmentPhaseValues(long id)
CmtReceiver
getCommitmentPhaseValues
in interface CmtReceiver
id
- get the commitment values according to this id.
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This is a fanpage dedicated to the Moomins!
MOOMIN MOOMIN MOOMIN
Feel free to click the buttons to find out more about the Moomins!


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sendMessage(String, String[], String[], String[], ArrayList<String>, String, String)
- Method in class com.datamotion.direct.
DMNet
Function call that sends a message
sendMessageEncoded(String, String[], String[], String[], ArrayList<String>, String, String)
- Method in class com.datamotion.direct.
DMNet
Function call that sends a message encoded
sendMIMEMessage(String, String)
- Method in interface com.certifiedmail.ssl.CMv4.
CMv4Soap
sendMIMEMessage(String, String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapProxy
sendMIMEMessage(String, String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapStub
sendMIMEMessageEncoded(String, String)
- Method in interface com.certifiedmail.ssl.CMv4.
CMv4Soap
sendMIMEMessageEncoded(String, String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapProxy
sendMIMEMessageEncoded(String, String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapStub
setCMv4SoapEndpointAddress(String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4Locator
setCMv4SoapWSDDServiceName(String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4Locator
setEndpoint(String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapProxy
setEndpoint(String)
- Method in class com.datamotion.direct.
DMNet
Function call that sets the cmv4 endpoint.
setEndpointAddress(String, String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4Locator
Set the endpoint address for the specified port name.
setEndpointAddress(QName, String)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4Locator
Set the endpoint address for the specified port name.
setInTransit(String, int, int, boolean)
- Method in interface com.certifiedmail.ssl.CMv4.
CMv4Soap
setInTransit(String, int, int, boolean)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapProxy
setInTransit(String, int, int, boolean)
- Method in class com.certifiedmail.ssl.CMv4.
CMv4SoapStub
setInTransit(String, int, int, boolean)
- Method in class com.datamotion.direct.
DMNet
Function call that sets a message's In Transit state
setMessage(String)
- Method in class com.datamotion.direct.
stackTrace
setStack(StackTraceElement[])
- Method in class com.datamotion.direct.
stackTrace
stackTrace
- Class in
com.datamotion.direct
stackTrace()
- Constructor for class com.datamotion.direct.
stackTrace
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{% extends "layout.html" %} {% block body %}
my subscription notifications
REFRESH TO UPDATE {% for table in tables %} {{ table|safe }} {% endfor %}After you receive a subscription notification, you can fetch all the data you need to determine if any action on your part is needed using the FHIR RESTful API. Below is a table which represents a graph of resource you may want to retreive and inspect:
| Source Profile | Path | Target Profile |
|---|---|---|
| US Core Encounter Profile | self | US Core Encounter Profile |
| US Core Encounter Profile | Encounter.location | US Core Location Profile |
| US Core Encounter Profile | Encounter.participant.individual | US Core Practitioner Profile |
| US Core Encounter Profile | Encounter.subject | US Core Patient Profile |
| US Core Coverage Profile | Coverage.beneficary | US Core Patient Profile |
| US Core Condition Profile | Condition.encounter | US Core Encounter Profile |
This data could be fetched using this sequence of RESTful queries:
Using the _include parameter to fetch the Encounter, Patient, Practitioner, and Location.
GET /Encounter/_id=[id]&_include=Encounter:patient&_include=Encounter:practitioner&_include=Encounter:location
Fetch the Condition data using the following query:
GET /Condition?patient=[patient id]&encounter=[encounter id]
Fetch the Coverage data using the following query:
GET /Coverage?patient=[patient id]


- f(double[], double) - Method in class ij.measure.CurveFitter
-
Returns the formula value for parameters 'p' at 'x'.
- f(int, double[], double) - Static method in class ij.measure.CurveFitter
-
Returns value of built-in 'fitType' formula value for parameters "p" at "x"
- f2hex(float) - Static method in class ij.util.Tools
-
Converts a float to an 9 byte hex string starting with '#'.
- FALSE - Static variable in interface ij.macro.MacroConstants
-
- FAST_TRACE - Static variable in class ij.macro.Interpreter
-
- FCOLOR - Static variable in class ij.Prefs
-
- FERET - Static variable in interface ij.measure.Measurements
-
- FERET - Static variable in class ij.measure.ResultsTable
-
- FERET_ANGLE - Static variable in class ij.measure.ResultsTable
-
- FERET_X - Static variable in class ij.measure.ResultsTable
-
- FERET_Y - Static variable in class ij.measure.ResultsTable
-
- FFT - Class in ij.plugin
-
This class implements the FFT, Inverse FFT and Redisplay Power Spectrum commands
in the Process/FFT submenu.
- FFT() - Constructor for class ij.plugin.FFT
-
- FFTCustomFilter - Class in ij.plugin.filter
-
This class implements the Process/FFT/Custom Filter command.
- FFTCustomFilter() - Constructor for class ij.plugin.filter.FFTCustomFilter
-
- FFTFilter - Class in ij.plugin.filter
-
This class implements the Process/FFT/Bandpass Filter command.
- FFTFilter() - Constructor for class ij.plugin.filter.FFTFilter
-
- FFTMath - Class in ij.plugin
-
The class implements the Process/FFT/Math command.
- FFTMath() - Constructor for class ij.plugin.FFTMath
-
- FHT - Class in ij.process
-
This class contains a Java implementation of the Fast Hartley
Transform.
- FHT(ImageProcessor) - Constructor for class ij.process.FHT
-
Constructs a FHT object from an ImageProcessor.
- FHT(ImageProcessor, boolean) - Constructor for class ij.process.FHT
-
- FHT() - Constructor for class ij.process.FHT
-
- FILE - Static variable in interface ij.macro.MacroConstants
-
- fileChanged() - Method in class ij.plugin.frame.Editor
-
- FileCircleFindingsPair - Class in craj.mapDigesterLocator
-
A pair of an image and a list of circles which where found in the image.
- FileCircleFindingsPair(File, List<CircleFinding>) - Constructor for class craj.mapDigesterLocator.FileCircleFindingsPair
-
Construct an FileCircleFindingsPair with the given file and
circle-findings.
- fileFormat - Variable in class ij.io.FileInfo
-
- FileInfo - Class in ij.io
-
This class consists of public fields that describe an image file.
- FileInfo() - Constructor for class ij.io.FileInfo
-
Creates a FileInfo object with all of its fields set to their default value.
- FileInfoVirtualStack - Class in ij.plugin
-
This plugin opens a multi-page TIFF file as a virtual stack.
- FileInfoVirtualStack() - Constructor for class ij.plugin.FileInfoVirtualStack
-
- FileInfoVirtualStack(FileInfo) - Constructor for class ij.plugin.FileInfoVirtualStack
-
- FileInfoVirtualStack(FileInfo, boolean) - Constructor for class ij.plugin.FileInfoVirtualStack
-
- fileName - Variable in class ij.io.FileInfo
-
- fileName - Static variable in class ij.plugin.FFT
-
- FileOpener - Class in ij.io
-
Opens or reverts an image specified by a FileInfo object.
- FileOpener(FileInfo) - Constructor for class ij.io.FileOpener
-
- FileSaver - Class in ij.io
-
Saves images in tiff, gif, jpeg, raw, zip and text format.
- FileSaver(ImagePlus) - Constructor for class ij.io.FileSaver
-
Constructs a FileSaver from an ImagePlus.
- fileType - Variable in class ij.io.FileInfo
-
- FILL - Static variable in interface ij.macro.MacroConstants
-
- fill(ImageProcessor) - Method in class ij.plugin.filter.Filler
-
Deprecated.
replaced by ImageProcessor.fill(Roi)
- fill(ImageProcessor) - Method in class ij.process.ByteProcessor
-
Fills pixels that are within roi and part of the mask.
- fill(ImageProcessor) - Method in class ij.process.ColorProcessor
-
Fills pixels that are within roi and part of the mask.
- fill() - Method in class ij.process.ColorProcessor
-
Fills the current rectangular ROI.
- fill() - Method in class ij.process.FloatProcessor
-
Fills the current rectangular ROI.
- fill(ImageProcessor) - Method in class ij.process.FloatProcessor
-
Fills pixels that are within roi and part of the mask.
- fill(int, int) - Method in class ij.process.FloodFiller
-
Does a 4-connected flood fill using the current fill/draw
value, which is defined by ImageProcessor.setValue().
- fill() - Method in class ij.process.ImageProcessor
-
Fills the image or ROI bounding rectangle with the current fill/draw value.
- fill(ImageProcessor) - Method in class ij.process.ImageProcessor
-
Fills pixels that are within the ROI bounding rectangle and part of
the mask (i.e. pixels that have a value=BLACK in the mask array).
- fill(Roi) - Method in class ij.process.ImageProcessor
-
Fills the ROI with the current fill/draw value.
- fill(ImageProcessor, Rectangle) - Method in class ij.process.PolygonFiller
-
Fills the polygon using the ImageProcessor's current drawing color.
- fill() - Method in class ij.process.ShortProcessor
-
Fills the current rectangular ROI.
- fill(ImageProcessor) - Method in class ij.process.ShortProcessor
-
Fills pixels that are within roi and part of the mask.
- fill8(int, int) - Method in class ij.process.FloodFiller
-
Does a 8-connected flood fill using the current fill/draw
value, which is defined by ImageProcessor.setValue().
- FILL_BLACK - Static variable in class ij.gui.NewImage
-
- FILL_COLOR - Static variable in class ij.io.RoiDecoder
-
- FILL_OVAL - Static variable in interface ij.macro.MacroConstants
-
- FILL_RAMP - Static variable in class ij.gui.NewImage
-
- FILL_RANDOM - Static variable in class ij.gui.NewImage
-
- FILL_RECT - Static variable in interface ij.macro.MacroConstants
-
- FILL_WHITE - Static variable in class ij.gui.NewImage
-
- FILLED - Static variable in class ij.gui.Arrow
-
- Filler - Class in ij.plugin.filter
-
This plugin implements ImageJ's Fill, Clear, Clear Outside and Draw commands.
- Filler() - Constructor for class ij.plugin.filter.Filler
-
- fillOutside(Roi) - Method in class ij.process.ImageProcessor
-
Fills outside an Roi.
- fillOval(int, int, int, int) - Method in class ij.process.ImageProcessor
-
Fills an elliptical shape.
- fillPolygon(Polygon) - Method in class ij.process.ImageProcessor
-
Fills a polygon.
- filter(ImageStack, int, float, float, float) - Static method in class ij.plugin.Filters3D
-
- filter(int) - Method in class ij.process.ByteProcessor
-
Filters using a 3x3 neighborhood.
- filter(int) - Method in class ij.process.ColorProcessor
-
3x3 unweighted smoothing.
- filter(int) - Method in class ij.process.FloatProcessor
-
Filters using a 3x3 neighborhood.
- filter(int) - Method in class ij.process.ImageProcessor
-
A 3x3 filter operation, where the argument (BLUR_MORE, FIND_EDGES,
MEDIAN_FILTER, MIN or MAX) determines the filter type.
- filter(int) - Method in class ij.process.ShortProcessor
-
Filters using a 3x3 neighborhood.
- FILTER - Static variable in class ij.Undo
-
- filter3D(ImageStack, float, float, float, int, int, int) - Method in class ij.process.StackProcessor
-
3D filter using threads
- FILTER_MAX - Static variable in class ij.process.StackProcessor
-
- FILTER_MAXLOCAL - Static variable in class ij.process.StackProcessor
-
- FILTER_MEAN - Static variable in class ij.process.StackProcessor
-
- FILTER_MEDIAN - Static variable in class ij.process.StackProcessor
-
- FILTER_MIN - Static variable in class ij.process.StackProcessor
-
- FILTER_VAR - Static variable in class ij.process.StackProcessor
-
- filterRGB(int, double) - Method in class ij.process.ColorProcessor
-
Performs the specified filter on the red, green and blue planes of this
image.
- Filters - Class in ij.plugin.filter
-
This plugin implements the Invert, Smooth, Sharpen, Find Edges,
and Add Noise commands.
- Filters() - Constructor for class ij.plugin.filter.Filters
-
- Filters3D - Class in ij.plugin
-
- Filters3D() - Constructor for class ij.plugin.Filters3D
-
- FILTERS_MENU - Static variable in class ij.Menus
-
- FINAL_PROCESSING - Static variable in interface ij.plugin.filter.PlugInFilter
-
Set this flag if the setup method of the filter should be called again after
the calls to the run(ip) have finished.
- FIND_EDGES - Static variable in class ij.process.ImageProcessor
-
- findAllMenuItems() - Method in class ij.plugin.CommandFinder
-
- findEdges() - Method in class ij.process.ColorProcessor
-
- findEdges() - Method in class ij.process.ImageProcessor
-
Finds edges in the image or ROI using a Sobel operator.
- findMaxima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
-
Calculates peak positions of 1D array N.Vischer, 13-sep-2013
- findMaxima(ImageProcessor, double, double, int, boolean, boolean) - Method in class ij.plugin.filter.MaximumFinder
-
Here the processing is done: Find the maxima of an image (does not find minima).
- findMinAndMax() - Method in class ij.process.FloatProcessor
-
Calculates the minimum and maximum pixel value for the entire image.
- findMinAndMax() - Method in class ij.process.ShortProcessor
-
- findMinima(double[], double, boolean) - Static method in class ij.plugin.filter.MaximumFinder
-
Returns minimum positions of array xx, sorted with decreasing strength
- findNthLowestNumber(float[], int, int) - Static method in class ij.plugin.filter.RankFilters
-
Find the n-th lowest number in part of an array
- FIT - Static variable in interface ij.macro.MacroConstants
-
- fit(ImageProcessor, ImageStatistics) - Method in class ij.process.EllipseFitter
-
Fits an ellipse to the current ROI.
- fitList - Static variable in class ij.measure.CurveFitter
-
Names of the built-in fit functions
- FITS - Static variable in class ij.io.FileInfo
-
- FITS - Static variable in class ij.io.Opener
-
- FITS_Reader - Class in ij.plugin
-
Opens and displays FITS images.
- FITS_Reader() - Constructor for class ij.plugin.FITS_Reader
-
- FITS_Writer - Class in ij.plugin
-
This plugin saves a 16 or 32 bit image in FITS format.
- FITS_Writer() - Constructor for class ij.plugin.FITS_Writer
-
- fitSpline(int) - Method in class ij.gui.PolygonRoi
-
- fitSpline() - Method in class ij.gui.PolygonRoi
-
- fitSplineForStraightening() - Method in class ij.gui.PolygonRoi
-
- Fitter - Class in ij.plugin.frame
-
ImageJ plugin that does curve fitting using the modified CurveFitter class.
- Fitter() - Constructor for class ij.plugin.frame.Fitter
-
- fitToWindow() - Method in class ij.gui.ImageCanvas
-
- fix(Scrollbar) - Static method in class ij.gui.GUI
-
Lightens overly dark scrollbar background on Windows 8.
- fixLineEndings() - Method in class ij.plugin.frame.Editor
-
Changes Mac OS 9 (CR) and Windows (CRLF) line separators to line feeds (LF).
- fixNewLines(String) - Static method in class ij.util.Tools
-
Converts carriage returns to line feeds.
- flatten() - Method in class ij.ImagePlus
-
Returns a "flattened" version of this image, in RGB format.
- flipHorizontal() - Method in class ij.process.ImageProcessor
-
Flips the image or ROI horizontally.
- flipHorizontal() - Method in class ij.process.StackProcessor
-
- flipStack(ImagePlus) - Method in class ij.plugin.StackReverser
-
- flipVertical() - Method in class ij.process.ByteProcessor
-
- flipVertical() - Method in class ij.process.ColorProcessor
-
- flipVertical() - Method in class ij.process.FloatProcessor
-
- flipVertical() - Method in class ij.process.ImageProcessor
-
Flips the image or ROI vertically.
- flipVertical() - Method in class ij.process.ShortProcessor
-
- flipVertical() - Method in class ij.process.StackProcessor
-
- flipXZ - Static variable in class ij.Prefs
-
Rotate XZ orthogonal views 180 degrees
- fList - Static variable in class ij.measure.CurveFitter
-
Equations of the built-in fit functions
- FLOAT - Static variable in class ij.plugin.filter.EDM
-
Output type: new 32-bit image
- FLOAT_STROKE_WIDTH - Static variable in class ij.io.RoiDecoder
-
- FloatBlitter - Class in ij.process
-
This class does bit blitting of 32-bit floating-point images.
- FloatBlitter(FloatProcessor) - Constructor for class ij.process.FloatBlitter
-
Constructs a FloatBlitter from a FloatProcessor.
- FloatPolygon - Class in ij.process
-
Used by the Roi classes to return float coordinate arrays and to
determine if a point is inside or outside of spline fitted selections.
- FloatPolygon() - Constructor for class ij.process.FloatPolygon
-
Constructs an empty FloatPolygon.
- FloatPolygon(float[], float[]) - Constructor for class ij.process.FloatPolygon
-
Constructs a FloatPolygon from x and y arrays.
- FloatPolygon(float[], float[], int) - Constructor for class ij.process.FloatPolygon
-
Constructs a FloatPolygon from x and y arrays.
- FloatProcessor - Class in ij.process
-
This is an 32-bit floating-point image and methods that operate on that image.
- FloatProcessor(int, int, float[]) - Constructor for class ij.process.FloatProcessor
-
Creates a new FloatProcessor using the specified pixel array.
- FloatProcessor(int, int, float[], ColorModel) - Constructor for class ij.process.FloatProcessor
-
Creates a new FloatProcessor using the specified pixel array and ColorModel.
- FloatProcessor(int, int) - Constructor for class ij.process.FloatProcessor
-
Creates a blank FloatProcessor using the default grayscale LUT that
displays zero as black.
- FloatProcessor(int, int, int[]) - Constructor for class ij.process.FloatProcessor
-
Creates a FloatProcessor from an int array using the default grayscale LUT.
- FloatProcessor(int, int, double[]) - Constructor for class ij.process.FloatProcessor
-
Creates a FloatProcessor from a double array using the default grayscale LUT.
- FloatProcessor(float[][]) - Constructor for class ij.process.FloatProcessor
-
Creates a FloatProcessor from a 2D float array using the default LUT.
- FloatProcessor(int[][]) - Constructor for class ij.process.FloatProcessor
-
Creates a FloatProcessor from a 2D int array.
- FloatStatistics - Class in ij.process
-
32-bit (float) image statistics, including histogram.
- FloatStatistics(ImageProcessor) - Constructor for class ij.process.FloatStatistics
-
Constructs an ImageStatistics object from a FloatProcessor
using the standard measurement options (area, mean,
mode, min and max).
- FloatStatistics(ImageProcessor, int, Calibration) - Constructor for class ij.process.FloatStatistics
-
Constructs a FloatStatistics object from a FloatProcessor
using the specified measurement options.
- FLOOD_FILL - Static variable in interface ij.macro.MacroConstants
-
- FloodFiller - Class in ij.process
-
This class, which does flood filling, is used by the floodFill() macro function and
by the particle analyzer
The Wikipedia at "http://en.wikipedia.org/wiki/Flood_fill" has a good
description of the algorithm used here as well as examples in C and Java.
- FloodFiller(ImageProcessor) - Constructor for class ij.process.FloodFiller
-
- FLOOR - Static variable in interface ij.macro.MacroConstants
-
- flush() - Method in class ij.ImagePlus
-
Sets the ImageProcessor, Roi, AWT Image and stack image
arrays to null.
- flush() - Method in class ij.io.LogStream
-
- focusGained(FocusEvent) - Method in class ij.gui.GenericDialog
-
- focusGained(FocusEvent) - Method in class ij.gui.ImageWindow
-
- focusGained(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
-
- focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
-
- focusGained(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
-
- focusGained(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
-
- focusGained(FocusEvent) - Method in class ij.plugin.Scaler
-
- focusGained(FocusEvent) - Method in class ij.text.TextWindow
-
- focusLost(FocusEvent) - Method in class ij.gui.GenericDialog
-
- focusLost(FocusEvent) - Method in class ij.gui.ImageWindow
-
- focusLost(FocusEvent) - Method in class ij.plugin.frame.ColorThresholder
-
- focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInDialog
-
- focusLost(FocusEvent) - Method in class ij.plugin.frame.PlugInFrame
-
- focusLost(FocusEvent) - Method in class ij.plugin.Orthogonal_Views
-
- focusLost(FocusEvent) - Method in class ij.plugin.Scaler
-
- focusLost(FocusEvent) - Method in class ij.text.TextWindow
-
- FolderOpener - Class in ij.plugin
-
Implements the File/Import/Image Sequence command, which
opens a folder of images as a stack.
- FolderOpener() - Constructor for class ij.plugin.FolderOpener
-
- Fonts - Class in ij.plugin.frame
-
Displays a window that allows the user to set the font, size and style.
- Fonts() - Constructor for class ij.plugin.frame.Fonts
-
- FOR - Static variable in interface ij.macro.MacroConstants
-
- FOREGROUND_COLOR_CHANGED - Static variable in interface ij.IJEventListener
-
- FOUR_CONNECTED - Static variable in class ij.gui.Wand
-
Wand operation type: trace outline of 4-connected pixels
- FOUR_CONNECTED - Static variable in class ij.plugin.filter.ParticleAnalyzer
-
Use 4-connected particle tracing.
- fps - Variable in class ij.measure.Calibration
-
Frame rate in frames per second
- FPS - Static variable in class ij.Prefs
-
- FractalBoxCounter - Class in ij.plugin.filter
-
Calculate the so-called "capacity" fractal dimension.
- FractalBoxCounter() - Constructor for class ij.plugin.filter.FractalBoxCounter
-
- FRAME - Static variable in class ij.measure.ResultsTable
-
- frameInterval - Variable in class ij.io.FileInfo
-
- frameInterval - Variable in class ij.measure.Calibration
-
Frame interval in 'timeUnit's
- FreehandRoi - Class in ij.gui
-
Freehand region of interest or freehand line of interest
- FreehandRoi(int, int, ImagePlus) - Constructor for class ij.gui.FreehandRoi
-
- FREELINE - Static variable in class ij.gui.Roi
-
- FREELINE - Static variable in class ij.gui.Toolbar
-
- freeMemory() - Static method in class ij.IJ
-
Runs the garbage collector and returns a string something
like "64K of 256MB (25%)" that shows how much of
the available memory is in use.
- FREEROI - Static variable in class ij.gui.Roi
-
- FREEROI - Static variable in class ij.gui.Toolbar
-
- FROM_CHAR_CODE - Static variable in interface ij.macro.MacroConstants
-
- FUNCTION - Static variable in interface ij.macro.MacroConstants
-
- FunctionFinder - Class in ij.macro
-
This class implements the text editor's Macros/Find Functions command.
- FunctionFinder() - Constructor for class ij.macro.FunctionFinder
-
- functionIDs - Static variable in interface ij.macro.MacroConstants
-
- Functions - Class in ij.macro
-
This class implements the built-in macro functions.
- functions - Static variable in interface ij.macro.MacroConstants
-


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--- title: Export to modules keywords: fastai sidebar: home_sidebar summary: "The functions that transform notebooks in a library" description: "The functions that transform notebooks in a library" nb_path: "nbs/00_export.ipynb" ---
The most important function defined in this module is notebooks2script
, so you may want to jump to it before scrolling though the rest, which explain the details behind the scenes of the conversion from notebooks to library. The main things to remember are:
# export
or %nbdev_export
flag on each cell you want exported# exports
or %nbdev_export_and_show
flag on each cell you want exported with the source code shown in the docs # exporti
or %nbdev_export_internal
flag on each cell you want exported without it being added to __all__
, and without it showing up in the docs.# default_exp
or %nbdev_default_export
flag followed by the name of the module (with points for submodules and without the py extension) everything should be exported in (if one specific cell needs to be exported in a different module, just indicate it after the %nbdev_export
flag: %nbdev_export special.module
)__all__
automatically__all__
if it's not picked automatically, write an exported cell with something like %nbdev_add2all "my_name"
For bootstrapping nbdev
we have a few basic foundations defined in imports
, which we test a show here. First, a simple config file class, Config
that read the content of your settings.ini
file and make it accessible:
create_config("github", "nbdev", user='fastai', path='..', tst_flags='tst', cfg_name='test_settings.ini')
cfg = Config(cfg_name='test_settings.ini')
test_eq(cfg.lib_name, 'nbdev')
test_eq(cfg.git_url, "https://github.com/fastai/nbdev/tree/master/")
test_eq(cfg.lib_path, Path.cwd().parent/'nbdev')
test_eq(cfg.nbs_path, Path.cwd())
test_eq(cfg.doc_path, Path.cwd().parent/'docs')
test_eq(cfg.custom_sidebar, 'False')
We derive some useful variables to check what environment we're in:
if not os.environ.get("IN_TEST", None):
assert IN_NOTEBOOK
assert not IN_COLAB
assert IN_IPYTHON
Then we have a few util functions.
test_eq(last_index(1, [1,2,1,3,1,4]), 4)
test_eq(last_index(2, [1,2,1,3,1,4]), 1)
test_eq(last_index(5, [1,2,1,3,1,4]), -1)
f1 = lambda o,p=0: (o*2)+p
f2 = lambda o,p=1: (o+1)/p
test_eq(f2(f1(3)), compose(f1,f2)(3))
test_eq(f2(f1(3,p=3),p=3), compose(f1,f2)(3,p=3))
test_eq(f2(f1(3, 3), 3), compose(f1,f2)(3, 3))
import time,random
def add_one(x, a=1):
time.sleep(random.random()/100)
return x+a
inp,exp = range(50),range(1,51)
test_eq(parallel(add_one, inp, n_workers=2), list(exp))
test_eq(parallel(add_one, inp, n_workers=0), list(exp))
test_eq(parallel(add_one, inp, n_workers=1, a=2), list(range(2,52)))
test_eq(parallel(add_one, inp, n_workers=0, a=2), list(range(2,52)))
A jupyter notebook is a json file behind the scenes. We can just read it with the json module, which will return a nested dictionary of dictionaries/lists of dictionaries, but there are some small differences between reading the json and using the tools from nbformat
so we'll use this one.
fname
can be a string or a pathlib object.
test_nb = read_nb('00_export.ipynb')
The root has four keys: cells
contains the cells of the notebook, metadata
some stuff around the version of python used to execute the notebook, nbformat
and nbformat_minor
the version of nbformat.
test_nb.keys()
test_nb['metadata']
f"{test_nb['nbformat']}.{test_nb['nbformat_minor']}"
The cells key then contains a list of cells. Each one is a new dictionary that contains entries like the type (code or markdown), the source (what is written in the cell) and the output (for code cells).
test_nb['cells'][0]
The following functions are used to catch the flags used in the code cells.
pat
can be a string or a compiled regex, if code_only=True
, this function ignores markdown cells.
cell = test_nb['cells'][1].copy()
assert check_re(cell, '%nbdev_export') is not None
assert check_re(cell, re.compile('%nbdev_export')) is not None
assert check_re(cell, '# bla') is None
cell['cell_type'] = 'markdown'
assert check_re(cell, '%nbdev_export') is None
assert check_re(cell, '%nbdev_export', code_only=False) is not None
cell = test_nb['cells'][0].copy()
cell['source'] = "a b c"
assert check_re(cell, 'a') is not None
assert check_re(cell, 'd') is None
# show that searching with paterns ['d','b','a'] will match 'b'
# i.e. 'd' is not found and we don't search for 'a'
assert check_re_multi(cell, ['d','b','a']).span() == (2,3)
This function returns a regex object that can be used to find nbdev flags in multiline text
magic_flag
pass True to find magic flags, False to find comment flags,body
regex fragment to match one or more flags,n_params
number of flag parameters to match and catch (-1 for any number of params),comment
explains what the compiled regex should do.is_export
returns;
cell
is to be exported or False
for an internal exportNone
if cell
will not be exported.The cells to export are marked with an %nbdev_export
, %nbdev_export_and_show
or %nbdev_export_internal
flag, potentially with a module name where we want it exported. The default module is given in a cell of the form %nbdev_default_export bla
inside the notebook (usually at the top), though in this function, it needs the be passed (the final script will read the whole notebook to find it).
%nbdev_export
, %nbdev_export_and_show
or %nbdev_export_internal
will be exported to the default module%nbdev_export special.module
, %nbdev_export_and_show special.module
or %nbdev_export_internal special.module
will be exported in special.module (located in lib_name
/special/module.py)%nbdev_export
will have it's signature added to the documentation%nbdev_export_and_show
will additionally have it's source code added to the documentation%nbdev_export_internal
will not show up in the documentation, and will also not be added to __all__
.cell = test_nb['cells'][1].copy()
test_eq(is_export(cell, 'export'), ('export', True))
cell['source'] = "%nbdev_export\nfrom nbdev.imports import *"
test_eq(is_export(cell, 'export'), ('export', True))
cell['source'] = "# exports"
test_eq(is_export(cell, 'export'), ('export', True))
cell['source'] = "%nbdev_export_and_show"
test_eq(is_export(cell, 'export'), ('export', True))
cell['source'] = "# exporti"
test_eq(is_export(cell, 'export'), ('export', False))
cell['source'] = "%nbdev_export_internal"
test_eq(is_export(cell, 'export'), ('export', False))
cell['source'] = "# export mod"
test_eq(is_export(cell, 'export'), ('mod', True))
cell['source'] = "%nbdev_export mod\nfrom nbdev.imports import *"
test_eq(is_export(cell, 'export'), ('mod', True))
cell['source'] = "# export mod.file"
test_eq(is_export(cell, 'export'), (f'mod{os.path.sep}file', True))
cell['source'] = "%nbdev_export mod.file"
test_eq(is_export(cell, 'export'), (f'mod{os.path.sep}file', True))
cell['source'] = "# exporti mod.file"
test_eq(is_export(cell, 'export'), (f'mod{os.path.sep}file', False))
cell['source'] = "%nbdev_export_internal mod.file"
test_eq(is_export(cell, 'export'), (f'mod{os.path.sep}file', False))
cell['source'] = "# expt mod.file"
assert is_export(cell, 'export') is None
cell['source'] = "# exportmod.file"
assert is_export(cell, 'export') is None
cell['source'] = "# exportsmod.file"
assert is_export(cell, 'export') is None
cell['source'] = "%nbdev_export_and_showmod.file"
assert is_export(cell, 'export') is None
cell['source'] = "%nbdev_export_internalmod.file"
assert is_export(cell, 'export') is None
cell['source'] = "# exporti mod file"
assert is_export(cell, 'export') is None
cell['source'] = "%nbdev_export_internal mod file"
assert is_export(cell, 'export') is None
Stops at the first cell containing a # default_exp
or %nbdev_default_export
flag (if there are several) and returns the value behind. Returns None
if there are no cell with that code.
test_eq(find_default_export(test_nb['cells']), 'export')
assert find_default_export(test_nb['cells'][2:]) is None
Note: ReTstFlags
isn't used during export but is needed by export2html
and test
.
The following functions make a list of everything that is exported to prepare a proper __all__
for our exported module.
tst = _re_patch_func.search("""
@patch
@log_args(a=1)
def func(obj:Class):""")
tst, tst.groups()
This function only picks the zero-indented objects on the left side of an =, functions or classes (we don't want the class methods for instance) and excludes private names (that begin with _
) but no dunder names. It only returns func and class names (not the objects) when func_only=True
.
To work properly with fastai added python functionality, this function ignores function decorated with @typedispatch
(since they are defined multiple times) and unwraps properly functions decorated with @patch
.
test_eq(export_names("def my_func(x):\n pass\nclass MyClass():"), ["my_func", "MyClass"])
#Indented funcs are ignored (funcs inside a class)
test_eq(export_names(" def my_func(x):\n pass\nclass MyClass():"), ["MyClass"])
#Private funcs are ignored, dunder are not
test_eq(export_names("def _my_func():\n pass\nclass MyClass():"), ["MyClass"])
test_eq(export_names("__version__ = 1:\n pass\nclass MyClass():"), ["MyClass", "__version__"])
#trailing spaces
test_eq(export_names("def my_func ():\n pass\nclass MyClass():"), ["my_func", "MyClass"])
#class without parenthesis
test_eq(export_names("def my_func ():\n pass\nclass MyClass:"), ["my_func", "MyClass"])
#object and funcs
test_eq(export_names("def my_func ():\n pass\ndefault_bla=[]:"), ["my_func", "default_bla"])
test_eq(export_names("def my_func ():\n pass\ndefault_bla=[]:", func_only=True), ["my_func"])
#Private objects are ignored
test_eq(export_names("def my_func ():\n pass\n_default_bla = []:"), ["my_func"])
#Objects with dots are privates if one part is private
test_eq(export_names("def my_func ():\n pass\ndefault.bla = []:"), ["my_func", "default.bla"])
test_eq(export_names("def my_func ():\n pass\ndefault._bla = []:"), ["my_func"])
#Monkey-path with @patch are properly renamed
test_eq(export_names("@patch\ndef my_func(x:Class):\n pass"), ["Class.my_func"])
test_eq(export_names("@patch\ndef my_func(x:Class):\n pass", func_only=True), ["Class.my_func"])
test_eq(export_names("some code\n@patch\ndef my_func(x:Class, y):\n pass"), ["Class.my_func"])
test_eq(export_names("some code\n@patch\ndef my_func(x:(Class1,Class2), y):\n pass"), ["Class1.my_func", "Class2.my_func"])
#Check delegates
test_eq(export_names("@delegates(keep=True)\nclass someClass:\n pass"), ["someClass"])
#Typedispatch decorated functions shouldn't be added
test_eq(export_names("@patch\ndef my_func(x:Class):\n pass\n@typedispatch\ndef func(x: TensorImage): pass"), ["Class.my_func"])
#try, except and other keywords should not be picked up (these can look like object def with type annotation)
test_eq(export_names("try:\n a=1\nexcept:\n b=2"), [])
test_eq(export_names("try:\n this_might_work\nexcept:\n b=2"), [])
Sometimes objects are not picked to be automatically added to the __all__
of the module so you will need to add them manually. To do so, create an exported cell with the following code %nbdev_add2all "name", "name2"
Please note:
%nbdev_add2all
can be space and/or comma separated and don't have to be quoted# 'func', 'func2' and 'func3' will be added to `__all__`
%nbdev_add2all func, func2 func3
# you'll see warnings if any unquoted function names can't be found
__all__
# 'func2' won't get added to `__all__`
%nbdev_add2all 'func',
'func2'
%nbdev_add2all
in a cell will get picked up%nbdev_add2all ['func']
# `func2` won't get added to `__all__`
%nbdev_add2all ['func2']
%nbdev_add2all
s in a notebook by putting them in different cells.If you need a from __future__ import
in your library, you can export your cell with special comments:
#export
from __future__ import annotations
class ...
or magic flags:
from __future__ import annotations
%nbdev_export
class ...
Notice that %nbdev_export
is after the __future__
import. Because __future__
imports must occur at the beginning of the file, nbdev allows __future__
imports in the flags section of a cell.
When we say from
from lib_name.module.submodule import bla
in a notebook, it needs to be converted to something like
from .module.submodule import bla
or
from .submodule import bla
depending on where we are. This function deals with those imports renaming.
Note that import of the form
import lib_name.module
are left as is as the syntax import module
does not work for relative imports.
test_eq(relative_import('nbdev.core', Path.cwd()/'nbdev'/'data.py'), '.core')
test_eq(relative_import('nbdev.core', Path('nbdev')/'vision'/'data.py'), '..core')
test_eq(relative_import('nbdev.vision.transform', Path('nbdev')/'vision'/'data.py'), '.transform')
test_eq(relative_import('nbdev.notebook.core', Path('nbdev')/'data'/'external.py'), '..notebook.core')
test_eq(relative_import('nbdev.vision', Path('nbdev')/'vision'/'learner.py'), '.')
To be able to build back a correspondence between functions and the notebooks they are defined in, we need to store an index. It's done in the private module _nbdev
inside your library, and the following function are used to define it.
return_type
tells us if the tuple returned will contain list
s of lines or str
ings with line breaks.
If no magic flags are found, treat the first comment line as a flag
{% include image.html alt="split_flags_and_code example" align="left" max-width="450" file="/images/split_flags_and_code.png" %}
If magic flags are found, the flags part can contain multiple lines
{% include image.html alt="split_flags_and_code example" align="left" max-width="450" file="/images/split_flags_and_code_magic.png" %}
def _test_split_flags_and_code(expected_flags, expected_code):
cell = nbformat.v4.new_code_cell('\n'.join(expected_flags + expected_code))
test_eq((expected_flags, expected_code), split_flags_and_code(cell))
expected=('\n'.join(expected_flags), '\n'.join(expected_code))
test_eq(expected, split_flags_and_code(cell, str))
_test_split_flags_and_code([
'#export'],
['# TODO: write this function',
'def func(x): pass'])
A new module filename is created each time a notebook has a cell marked with %nbdev_default_export
. In your collection of notebooks, you should only have one notebook that creates a given module since they are re-created each time you do a library build (to ensure the library is clean). Note that any file you create manually will never be overwritten (unless it has the same name as one of the modules defined in a %nbdev_default_export
cell) so you are responsible to clean up those yourself.
fname
is the notebook that contained the %nbdev_default_export
cell.
Create module files for all %nbdev_default_export
flags found in files
and return a list containing the names of modules created.
Note: The number if modules returned will be less that the number of files passed in if files do not %nbdev_default_export
.
By creating all module files before calling _notebook2script
, the order of execution no longer matters - so you can now export to a notebook that is run "later".
You might still have problems when
%nbdev_default_export
yetin which case _notebook2script
will print warnings like;
Warning: Exporting to "core.py" but this module is not part of this build
If you see a warning like this
FileNotFoundError
with tempfile.TemporaryDirectory() as d:
os.makedirs(Path(d)/'a', exist_ok=True)
(Path(d)/'a'/'f.py').touch()
os.makedirs(Path(d)/'a/b', exist_ok=True)
(Path(d)/'a'/'b'/'f.py').touch()
add_init(d)
assert not (Path(d)/'__init__.py').exists()
for e in [Path(d)/'a', Path(d)/'a/b']:
assert (e/'__init__.py').exists()
Finds cells starting with %nbdev_export
and puts them into the appropriate module. If fname
is not specified, this will convert all notebook not beginning with an underscore in the nb_folder
defined in setting.ini
. Otherwise fname
can be a single filename or a glob expression.
silent
makes the command not print any statement and to_dict
is used internally to convert the library to a dictionary.


Have a look in the console, we should have received data from GeoSpock.
Find out more at https://github.com/Geovation/GeoSpockWeb


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Index: R
- r command (sed)
: 5.11. Reading and Writing Files
- rand()
: 9.1.3. Random Number Generation
- random numbers
: 9.1.3. Random Number Generation
- range of characters
: (see character classes)
- --re-interval option (gawk)
: <IP_ADDRESS>. Command line options
- read command
: (see r command (sed))
- reading
: 10.1. The getline Function
- from files
- 5.11. Reading and Writing Files
- 10.1.1. Reading Input from Files
- from pipe
: 10.1.3. Reading Input from a Pipe
- readsource script (example)
: 13.6. readsource - Format Program Source Files for troff
- RECLEN variable (tawk)
: <IP_ADDRESS>. Tawk language extensions
- records, awk
- 2.4.1. Running awk
- 7.5. Records and Fields
- B.2.1. Records and Fields
- arrays and
: 8.4. Arrays
- fixed-length (tawk)
: <IP_ADDRESS>. Tawk language extensions
- multiline
: 7.7.1. Working with Multiline Records
- NF variable
: 7.7. System Variables
- NR variable
- 7.7. System Variables
- 8.4. Arrays
- 10.1.2. Assigning the Input to a Variable
- RT variable (gawk)
: <IP_ADDRESS>. Regular expression record terminators
- separators for
: (see delimiters)
- redirection
- <IP_ADDRESS>. Saving output
- 4.3. Testing and Saving Output
- 10.5. Directing Output to Files and Pipes
- references
: Other Sources of Information About sed and awk
- referencing fields
- 2.4.1. Running awk
- 7.5.1. Referencing and Separating Fields
- regular expressions
- 1.4. Four Hurdles to Mastering sed and awk
- 3. Understanding Regular Expression Syntax
- B.2.3. Patterns
- B.2.4. Regular Expressions
- (see also pattern matching)
- as constants
: 7.8. Relational and Boolean Operators
- delimiters for
- 2.1. Awk, by Sed and Grep, out of Ed
- 5.3. Substitution
- dynamic, faking
: 11.1.5. Faking Dynamic Regular Expressions
- ed and
: 2.1. Awk, by Sed and Grep, out of Ed
- examples of
: 3.3. I Never Metacharacter I Didn't Like
- gawk extensions to
: <IP_ADDRESS>. Extended regular expressions
- metacharacters for
: (see netacharacters)
- POSIX standard for
: <IP_ADDRESS>. POSIX character class additions
- RS variable as
- <IP_ADDRESS>. Regular expression record separators (gawk and mawk)
- <IP_ADDRESS>. Tawk language extensions
- tawk and
: <IP_ADDRESS>. Tawk language extensions
- union of
- 3.2. A Line-Up of Characters
- 3.2.9. Alternative Operations
- writing
: 3.2.3. Writing Regular Expressions
- relational expressions
: B.2.3. Patterns
- relational operators
: 7.8. Relational and Boolean Operators
- replacement metacharacters
: 5.3.1. Replacement Metacharacters
- numbered saves
: 5.3.1. Replacement Metacharacters
- replacing text
- 1.2. A Stream Editor
- <IP_ADDRESS>. The extent of the match
- retrieving data from files
: 7.11. Information Retrieval
- return statement
- 9.3. Writing Your Own Functions
- 9.3.1. Writing a Sort Function
- revision control systems
: 10.7.1. Make a Copy
- RS variable
: 7.7. System Variables
- regular expression for
- <IP_ADDRESS>. Regular expression record separators (gawk and mawk)
- <IP_ADDRESS>. Tawk language extensions
- RT variable (gawk)
: <IP_ADDRESS>. Regular expression record terminators
- rules, pattern-matching
: (see pattern matching)
Symbols
| A
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Copyright © 1998
O'Reilly & Associates, Inc.
All Rights Reserved.


We will assign a Monitoring Officer who will visit your project at this address.
An address line
You can change your project address up until your grant offer letter is generated.


Keest Dorst, Pieter E. Vermaas
"One of our tools of analysis is the distinction between structural and intentional descriptions of artefacts. In designing typically a transition occurs between these two types of description: functions or purposes, which may be seen as intentional descriptions of the artefact to be designed, are transformed in structural or physical descriptions of this artefacts."
"Designing starts— also by Gero’s description, as we will see—with a purpose (an intentional concept) and ends with a structural description of an artefact (Kroes and Meijers 2002)."


| Package | Description |
|---|---|
| edu.pjatk.inn.coffeemaker | |
| edu.pjatk.inn.coffeemaker.impl |
| Modifier and Type | Method and Description |
|---|---|
Recipe |
CoffeeMaking.getRecipeForName(java.lang.String name)
Returns the Recipe associated with the given name
|
Recipe[] |
CoffeeMaking.getRecipes()
Returns an array of all the getRecipes
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
CoffeeMaking.addRecipe(Recipe r)
Returns true if a recipe is successfully added to the
coffee maker
|
boolean |
CoffeeMaking.deleteRecipe(Recipe r)
Returns true if the recipe was deleted from the
coffee maker
|
boolean |
CoffeeMaking.editRecipe(Recipe oldRecipe,
Recipe newRecipe)
Returns true if the recipe is successfully edited
|
int |
CoffeeMaking.makeCoffee(Recipe r,
int amtPaid)
Returns the change of a user's beverage purchase, or
the user's money if the beverage cannot be made
|
| Modifier and Type | Method and Description |
|---|---|
static Recipe |
Recipe.getRecipe(Context context)
Method that returns object of recipe by setting its
fields from given context using metgods defined in this class
|
Recipe |
CoffeeMaker.getRecipeForName(java.lang.String name)
Returns the Recipe associated with the given name
|
Recipe[] |
CoffeeMaker.getRecipes()
Returns an array of all the getRecipes
|
| Modifier and Type | Method and Description |
|---|---|
boolean |
CoffeeMaker.addRecipe(Recipe r)
Returns true if a recipe is successfully added to the
coffee maker
|
boolean |
CoffeeMaker.deleteRecipe(Recipe r)
Returns true if the recipe was deleted from the
coffee maker
|
boolean |
CoffeeMaker.editRecipe(Recipe oldRecipe,
Recipe newRecipe)
Returns true if the recipe is successfully edited
|
boolean |
Inventory.enoughIngredients(Recipe r)
Returns true if there are enough ingredients to make
the beverage.
|
boolean |
Recipe.equals(Recipe r) |
static Context |
Recipe.getContext(Recipe recipe)
Method that creates context from given recipe by
using methods returning its values.
|
int |
CoffeeMaker.makeCoffee(Recipe r,
int amtPaid)
Returns the change of a user's beverage purchase, or
the user's money if the beverage cannot be made
|


Before Change
self.last_checked = time.time()
total_gb = psutil.virtual_memory().total / (1024**3)
used_gb = total_gb - psutil.virtual_memory().available / (1024**3)
if self.cgroup_memory_limit_gb < total_gb:
total_gb = self.cgroup_memory_limit_gb
with open("/sys/fs/cgroup/memory/memory.usage_in_bytes",
After Change
return // escape hatch, not intended for user use
self.last_checked = time.time()
psutil_mem = psutil.virtual_memory()
total_gb = psutil_mem.total / (1024**3)
used_gb = total_gb - psutil_mem.available / (1024**3)
// Linux, BSD has cached memory, which should
// also be considered as unused memory
if hasattr(psutil_mem, "cached"):
used_gb -= psutil_mem.cached / (1024**3)
if self.cgroup_memory_limit_gb < total_gb:
total_gb = self.cgroup_memory_limit_gb


Technical Overview¶
Introduction¶
We will cover here technical aspects of the viewer which are important for contributing to the project. It is worthwhile to begin by reviewing the Design Choices and Tradeoffs & Implications sections on the About page.
Building & Publishing¶
Build from source & install locally¶
cd tools
./rebuild
Clean up source builds¶
cd tools
./clean
Generate Sphinx documentation¶
cd tools
./mkdocs
Build from source and publish Linux (wheels and source)¶
cd tools
./publish_linux
Note: Requires Docker in order to build with manywheel
Build from source and publish Mac wheel¶
cd tools
./publish_mac
Viewer Use Cases¶
Viewer allows the following primary use cases:
Visualize & analyze time series data in a Jupyter Notebook
Work on a project of time series data in a web-based interface
Allow multi-user annotation of time series data in a web-based interface
Serve via intranet or internet
Detailed Viewer Use Cases¶
In detail, from a perspective of technical architecture, the following use cases are accommodated:
- Jupyter Notebook Interface
Visualize/explore time series data ad-hoc
Visualize/explore project data
Analyze project data
Analyze annotations
- Python Module
Add project data
Analyze project data
Analyze annotations
- Web Server
Visualize/explore and/or annotate project data in single-user mode
Perform analytical tasks (e.g. create & manage annotation assignments, etc.)
Multi-user visualization & annotation by human subject matter experts
Optional user authentication integration
Technical Documentation¶
Technical Architecture¶
AUViewer is comprised of: * A Python codebase in the form of a package built of modules, and * A static HTML/JS/CSS codebase which makes up the frontend web application.
The Python code is organized primarily around classes which represent the most important conceptual components of the data:
- Project
- File
- Series
DownsampleSet
RawData
Other conceptual components, in the backend, are represented exclusively by database models (e.g. models.Annotation, models.PatternSet, and models.Pattern). The differentiating factor is that the Python classes, while the application is running, are treated as the primary source of truth for the associated data, and the database is a persistence medium; whereas, for the conceptual components which are only represented by database models, the database is the source of truth while the application is running.
Other important Python technical components are: * Flask web server * Cython functions for downsampling * Database models and connectivity logic * Config module * Shared helper functions
Similar to Python, the web client JavaScript codebase is organized primarily around classes which represent the important conceptual components of the data:
- Project
- File
- AnnotationSet (extends Set)
Annotation (extends Member)
- AssignmentSet (extends Set)
Assignment (extends Member)
- PatternSet (extends Set)
Pattern (extends Member)
Graph
Additionally, a few technical components are implemented in classes:
GlobalStateManager (instantiated as a global variable globalStateManager)
RequestHandler (instantiated as a global variable requestHandler)
TemplateSystem (instantiated as a global variable templateSystem)
No persistence or caching layer is used by the frontend codebase.
Strategies¶
Because AUViewer is meant for visualization & annotation of large datasets, one important architectural strategy is to lazy load the data from disk (i.e. no caching in memory) with the exception of metadata which is not likely to grow too large for memory. For example, when the AUViewer web service starts, it loads the projects, file lists, and series lists but not the data contained therein. Each time an API request comes in to load a file, the data is read from disk, served, and then immediately purged from memory.
Patterns & Conventions¶
Communication between the web application frontend and backend takes place via an HTTP REST API interface using GET parameters for client-to-backend requests and JSON for backend-to-client responses. As a general design pattern, the classes (mentioned above) output generalized data structures (e.g. lists, dicts), and the encapsulation of response data into JSON takes place in the http handler functions in the serve module. This breakdown makes sense since AUViewer can be used both as a Python/Jupyter Notebook module and a web server.
As a function naming convention, getters are named get[Thing], but getters which return output structured primarily for web transmission are named get[Thing]Output (for API transmission) or get[Thing]Payload (for an initial data payload embedded in an html template).
Backend Configuration¶
Backend config consists of the following types of configuration parameters:
General settings (e.g. verbose output)
Tuning parameters (e.g. target data points per series transmission)
Asset locations
Web server configuration (e.g. root web directory, Flask config)
AUViewer comes with default config parameters for everything except the data directory location, which must be specified. Configuration is loaded and managed by the auviewer.config module.


Preparation time
less than 30 mins
Cooking time
10 to 30 mins
Serves
Serves 4
Dietary
This, thankfully, is a Thai recipe that doesn't require all the speciality ingredients that are sometimes so elusive. The list of ingredients seems rather long, but it is made in moments and has a lovely fragrant flavour.
Equipment and preparation: You will need a 9in/23cm frying pan with a close-fitting lid.
Begin by dissolving the creamed coconut in the boiling water, then place it in a food processor with the garlic, chillies, ginger and coriander stalks, whizzing until everything is finely chopped.
Leave this aside while you heat the oil over a gentle heat in the frying pan, then add the cinnamon sticks, cloves, peppercorns and cashew nuts to the pan and sauté everything gently for about 1 minute. Next, add the onions and continue to cook over a medium heat until they become softened and pale gold in colour, which will take 8-10 minutes. Next add the rice, then stir once and cook for another 2-3 minutes. After that, add the coconut mixture, give everything a stir, and cook for a further 2-3 minutes. Now add the peas, salt and hot water, bring it all up to a gentle simmer, then cover with the lid. Turn the heat to low and let everything cook very gently for 8 minutes; use a timer here, and don't lift the lid.
Then remove the pan from the heat, take the lid off and cover the pan with a cloth for 10 minutes before serving. Finally, remove the pieces of cinnamon, sprinkle in the lime juice and the finely chopped coriander leaves, then fork the rice gently to separate the grains. Garnish with the reserved whole coriander leaves.


| DOSE: |
13 capsls |
oral |
Yohimbe |
(ground / crushed) |
After delving into the realm of all the myriad legal highs mother nature offers us, I had decided to experiment with Yohimbe. I got a bottle of the stuff in capsule form from my local 'health' food store and started my first couple of trials around the recommended dosage.  Note, I do not recommend doing the following until you have gotten your basis with this substance and tried smaller doses. I popped about 13 of these capsules over a period of about 45 minutes which from what I've read is more than anyone else has reported. Me and my friends (who had taken smaller amounts) went skateboarding and we all noticed the stimulant effects. However, it seems like we had to stop and rest often because any activity while on this substance is going to make your heart go crazy.
We decided to go to a store and mess around.  This surprised me as I was skeptical of this claim. I even felt some of the back shivers that some ppl claim which is kinda neat to experience.  My heart was starting to go off like mad. I felt really hungry and ate some cheese sticks which tasted really good. I don't know if there has been any mention of this but I think yohimbe increases your appetite at least as much if not more than marijuana. After eating these I was really starting to feel sick. My heart was racing! I have done lots of stimulants including copious amounts of meth and I can say that nothing will speed your heart up like this stuff will. I had to lay down and did so right in the middle of the aisle. My heart was going so fast that I was exhausted and felt like I was on the verge of passing out.
I was beginning to regret the whole experience and was actually afraid that I might die from a heart attack. I felt very nauseous so I stood up and went to the bathroom where I threw up the undigested contents of the cheese sticks. I would not recommend eating cheese while on this stuff (possible reaction do to Yohimbe being an MAOI?). The rest of the experience culminated in me starting to come down and realize I wasn't going to die afterall. I think this substance is fun but can definitely be overdone. One more thing to note is that it was very hard to get high on weed while on large doses of Yohimbe.
Experience Reports are the writings and opinions of the individual authors who submit them.
Some of the activities described are dangerous and/or illegal and none are recommended by Erowid.


India closer to world’s first male contraceptive injection
- The Indian Council Medical Research (ICMR) is closer to having world's first male contraceptive as it complete its clinical trial
- When the drug is finally approved, it will be effective for 13 years in a male carrier before it loses its capacity
- It is said that men in India would prefer the injectable male contraceptive to surgical vasectomy that is presently obtainable
The Indian Council of Medical Research (ICMR) has successfully completed clinical trials of the world’s first injectable male contraceptive, and it has been sent to the Drug Controller General of India (DCGI) for approval.
According to Hindustantimes, if the birth control pill is finally approved, when injected it would be effective for 13 years in the carrier.
The same media also reports that injection is an alternative to the only form of male birth control which is surgical vasectomy.
It should be noted that the ICMR is the final body in India that oversees biomedical research and gets its funding from the government at the union ministry of health.
HT reports that 53.5% of Indian couples use birth spacing methods, out of permanent sterilization is the most popular.
Doctors in the country are of the opinion that injectable male contraceptives will be most demanded-for than surgical vasectomy as Dr Anup Kumar said men will opt for it.
“Non-surgical procedures are always preferred over surgical procedures because they will be safer and less invasive. More men are likely to opt for it,” he said.
There are, however, a challenge in the face of the drug once it gets approval; the government will need to publicise it for it to gain wide acceptability.
AR Nanda, a former family welfare secretary is one of the above opinion, adding that incentives for people who go for the option is also necessary.
PAY ATTENTION: Download our mobile app to enjoy the latest news update
“Two things are needed from the government for it to work; one is to make use of the trial subjects for awareness generation among masses about the product, and second is to offer higher incentives for people opting for male contraceptives,” Nanda said.
South West Development Commission bill scales first reading in Senate
Meanwhile, Legit.ng earlier reported that Mansurah Abdulazeez, a molecular biologist at the Center for Biotechnology Research, Bayero University, Kano, made a marvelous breakthrough in the treatment of cancer as she developed treatment from African plants.
NAIJ.com (naija.ng) -> Legit.ng We have upgraded to serve you better
I need help! Man with 14 children cries out | Legit TV


All of the Web services accept and return both XML or JSON formatted data.
A sample invocation of a web service using the 'curl' tool could look like this:
curl -k -v
--header "Accept:application/json"
-H "Content-Type:application/json"
-X PUT
-d @<datafilename>
"http://<USERNAME>:<PASSWORD>@<HOST_ADDRESS>/ui/THE_DESIRED_SERVICE"
- '<HOST_ADDRESS>' is the IP address or DNS name of the web service target device
- '<USERNAME>:<PASSWORD>' is the web service user credentials used to log in to the target device
- '/ui/DESIRED_SERVICE' is the web service URL to access
- The Accept header controls the response type (JSON or XML)
- The Content-Type header declares the format of the content in the data file you are PUTting (JSON or XML)
- The '-X PUT' says "generate a HTTP PUT request" (the default is HTTP GET request) PUT, POST, GET, and DELETE are supported as
defined by the documentation for the service you are invoking
- '-d @<datafilename>' specifies the name of the file (for example 'sample.json') that contains the JSON data to send
- The '-k' and '-v' are optional, used to show progress while debugging responses
The following sections supply details about the web services that are available on this device. You can collapse
and expand the sections below by clicking on the section header.
Help Web Services Documentation
Use these API methods to get help data about each web service module.


R/calcGU.R
calcGU.Rd
Genome Uniqueness Functions
calcGU(alleles, threshold = 1, byID = FALSE, pop = NULL)
| alleles | dataframe of containing an
|
|---|---|
| threshold | an integer indicating the maximum number of copies of an allele that can be present in the population for it to be considered rare. Default is 1. |
| byID | logical variable of length 1 that is passed through to
eventually be used by |
| pop | character vector with animal IDs to consider as the population of interest, otherwise all animals will be considered. The default is NULL. |
Dataframe rows: id, col: gu
A single-column table of genome uniqueness values as percentages.
Rownames are set to 'id' values that are part of the population.
Part of Genetic Value Analysis
The following functions calculate genome uniqueness according to the equation described in Ballou & Lacy.
It should be noted, however that this function differs slightly in that it does not distinguish between founders and non-founders in calculating the statistic.
Ballou & Lacy describe genome uniqueness as "the proportion of simulations in which an individual receives the only copy of a founder allele." We have interpreted this as meaning that genome uniqueness should only be calculated for living, non-founder animals. Alleles possessed by living founders are not considered when calculating genome uniqueness.
We have a differing view on this, since a living founder can still contribute to the population. The function below calculates genome uniqueness for all living animals and considers all alleles. It does not ignore living founders and their alleles.
Our results for genome uniqueness will, therefore differ slightly from those returned by Pedscope. Pedscope calculates genome uniqueness only for non-founders and ignores the contribution of any founders in the population. This will cause Pedscope's genome uniqueness estimates to possibly be slightly higher for non-founders than what this function will calculate.
The estimates of genome uniqueness for founders within the population calculated by this function should match the "founder genome uniqueness" measure calculated by Pedscope.
Ballou JD, Lacy RC. 1995. Identifying genetically important individuals for management of genetic variation in pedigreed populations, p 77-111. In: Ballou JD, Gilpin M, Foose TJ, editors. Population management for survival and recovery. New York (NY): Columbia University Press.
# \donttest{ library(nprcgenekeepr) ped1Alleles <- nprcgenekeepr::ped1Alleles gu_1 <- calcGU(ped1Alleles, threshold = 1, byID = FALSE, pop = NULL) gu_2 <- calcGU(ped1Alleles, threshold = 3, byID = FALSE, pop = NULL) gu_3 <- calcGU(ped1Alleles, threshold = 3, byID = FALSE, pop = ped1Alleles$id[20:60]) # }


Customize this mustache template code, and insert it into your HTML. This code uses your read key.
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Because we have been in your shoes, and we know what it's like being used and duped all in a bid to create something for oneself. We are doing this to give back to the society by showing the people how to fish, instead of sharing fish. We are doing this as our own contribution to national development. If the country will grow, the people must first grow.
Have you ever suffered? Then you will understand Femi Adetayo's story.
Femi Adetayo is from a lower class Nigerian family that could only provide what they really needed for themselves. He was always used to taking the cheapest option not because he was miserly, but because that was what he could afford, up until 4 (four) years ago.
He decided to go into business four years ago when he saw that garri was cheaper in Ondo state (where he studied), compared to Lagos. From food stuffs, he moved into Made in Naija shoe and belt business. He was only able to break even with these. Despite the hard work, he was still struggling. He wanted more. He needed more. So, he decided to sell more fashion items from known brands because they were in higher demand. He bought from Wholesalers and resold with a little profit for himself. It still wasn't enough.
He was so curious to know how the wholesalers got the products and were making so much money. He tried so hard to learn but he lost a lot of money going the wrong way, and paying the wrong people. He was used and duped over and over. He didn't give up until he found the right channel! When he did, he invested both time and money into learning how to import goods from various countries of the world himself without using middlemen or agents. THIS WAS HIS BIG BREAK!!
Since Femi Adetayo started importing directly from international suppliers, his business began to boom. He learnt more about business and now he owns luxury fashion stores across Lagos. One on the mainland, and two others on the Island.
Today, Femi Adetayo is a Premium Luxury Fashion Shopper, who has made millions and millions of naira from his fast growing business. He has given himself to teaching and equipping Nigerians will profitable skillset that can eradicate poverty in their lineage.


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- Source:
Members
(static, constant) exports.app :JQuery.<HTMLDivElement>
The default app selector.
Type:
- JQuery.<HTMLDivElement>
- Source:
Methods
(static) easeInOutQuad(t, b, c, d) → {number}
Creates a smooth ease in out quad for javascript animations.
Parameters:
| Name | Type | Description |
|---|---|---|
t |
number |
the progress of a animation |
b |
number |
the start of a animation |
c |
number |
the difference between the end and start of animation |
d |
number | the animation duration |
- Source:
Returns:
- the smooth value of the animation
- Type
- number
(static) exports.backtop(selector, options)
Creates a back-top component from a jQuery selector.
Parameters:
| Name | Type | Description |
|---|---|---|
selector |
string |
jquery selector for the element |
options |
Object |
the options are optionals. Offset is the height at which it shows and the scroll duration is the time the animation takes to go back to the top. |
- Source:
(static) exports.createBacktop() → {JQuery.<HTMLAnchorElement>}
Creates a backtop component. The backtop creates a button that brings the user back to the top of the page when clicked.
- Source:
Returns:
- returns a jquery element of the backtop.
- Type
- JQuery.<HTMLAnchorElement>
(static) exports.createHero() → {JQuery.<HTMLElement>}
Creates the default hero for the home page. The hero section contains the button to play the game.
- Source:
Returns:
- returns a section jquery element
- Type
- JQuery.<HTMLElement>
(static) exports.createLeaderboard(list) → {JQuery.<HTMLElement>}
Creates the leaderboard component with a list of
createScore
if their is players or
createNoScore
if no scores have been registered to
the leaderboard.
Parameters:
| Name | Type | Description |
|---|---|---|
list |
Array.<Leaderboard> | the leaderboard list |
- Source:
Returns:
- jquery element of the leaderboard component.
- Type
- JQuery.<HTMLElement>
(static) exports.createModal(nameopt, titleopt, subtitleopt, buttonopt, emojiopt, infoopt) → {JQuery.<HTMLDivElement>}
Creates a modal component with properties.
Parameters:
| Name | Type | Attributes | Description |
|---|---|---|---|
name |
string | <optional> |
the name of the player |
title |
string | <optional> |
the title of the modal |
subtitle |
string | <optional> |
the subtitle of the modal |
button |
string | <optional> |
the button text of the confirmation |
emoji |
string | <optional> |
the title emoji |
info |
string | <optional> |
the score of the player |
- Source:
Returns:
- returns a jquery element of a modal
- Type
- JQuery.<HTMLDivElement>
(static) exports.createNoScore() → {string}
Creates the no score component if the leaderboard
's
list is empty.
- Source:
Returns:
-
the no score component if the
leaderboard
is empty
- Type
- string
(static) exports.createScore(player, index) → {string}
Creates the score component used inside the
createLeaderboard
component.
Parameters:
| Name | Type | Description |
|---|---|---|
player |
Leaderboard |
the player in the leaderboard |
index |
number |
the index of the player on the leaderboard |
- Source:
Returns:
- the score component in a string format.
- Type
- string
(static) exports.eventCloseButton()
Triggers a event when the close button is clicked.
Note: emits the modalclose
event
- Source:
(static) exports.eventModal()
Generates all the events for the modal component.
- Source:
(static) exports.eventModalClose()
Listen to modalclose
event to apply the actions when
a modal closes.
- Source:
(static) exports.eventModalError()
Listens to the modalerror
event and sets the message
to the error element in the dom on the modal.
- Source:
(static) exports.eventModalOpen()
Listens to the modalopen
event on the modal to make
sure the modal opens when needed.
- Source:
(static) exports.eventModalStart()
Listens to the modalstart
event to start the game.
- Source:
(static) exports.eventPlayButton()
Triggers a event when the play button is clicked.
Note: emits the modalopen
event
- Source:
(static) exports.eventStartButton()
Triggers a event when the start button is clicked.
Note: emits the modalstart
event
- Source:
(static) exports.fade(selector) → {jQuery}
jQuery fade animation to a selector.
Parameters:
| Name | Type | Description |
|---|---|---|
selector |
string | the selector to fade |
- Source:
Returns:
- a jquery element of the selector
- Type
- jQuery
(static) exports.leftAnimation(selector) → {jQuery}
jQuery left animation to animate a selector from a left position.
Parameters:
| Name | Type | Description |
|---|---|---|
selector |
string | the selector to animate |
- Source:
Returns:
- a jquery element of the selector
- Type
- jQuery
(static) exports.parallax()
Creates a parallax component by modifying the css variables used for scrolling y.
- Source:
(static) mouseParallax(selector) → {function}
Adds a mouse event to apply a parallax effect on the mouse.
Parameters:
| Name | Type | Description |
|---|---|---|
selector |
string | hello |
- Source:
Returns:
- returns a function with the
mousemove
event.
- Type
- function
(static) scrollParallax(varName, speed, limit)
Adds the scroll parallax to a CSS Variable.
Parameters:
| Name | Type | Default | Description |
|---|---|---|---|
varName |
string | the CSS Variable name |
|
speed |
number |
the speed of the parallax |
|
limit |
number | 330 | the limit of the screen |
- Source:
(static) scrollTo(final, duration, cbopt)
Scrolls to a specified y position in a certain duration. Makes the scroll smooth.
Parameters:
| Name | Type | Attributes | Description |
|---|---|---|---|
final |
number | the final y value |
|
duration |
number | the duration in ms |
|
cb |
function | <optional> |
a callback when it has scroll to the position |
- Source:


| Name | Description |
| connectedToMaster |
The normal operating state for a slave host. In this state,
the host is exchanging heartbeats with a master over
the management network, and is thus connected to it. If
there is a management network partition, the slave will be
in this state only if it is in the same partition as the master.
This state is reported by the master of a slave host.
|
| election |
The Fault Domain Manager on the host has been initialized and
the host is either waiting to join the existing master or
is participating in an election for a new master. This state
is reported by vCenter Server or by the host itself.
|
| fdmUnreachable |
The Fault Domain Manager (FDM) on the host cannot be reached. This
state is reported in two unlikley situations.
- First, it is reported by
a master if the host responds to ICMP pings sent by the master over the
management network but the FDM on the host cannot be reached by the master.
This situation will occur if the FDM is unable to run or exit the
uninitialized state.
- Second, it is reported by vCenter Server if it cannot connect to a
master nor the FDM for the host. This situation would occur if all hosts
in the cluster failed but vCenter Server is still running. It may also
occur if all FDMs are unable to run or exit the uninitialized state.
|
| hostDown |
The slave host appears to be down. This state is reported by the
master of a slave host.
|
| initializationError |
An error occurred when initilizating the Fault Domain Manager
on a host due to a problem with installing the
agent or configuring it. This condition can often be cleared by
reconfiguring HA for the host. This state is reported by vCenter
Server.
|
| master |
The Fault Domain Manager on the host has been elected a
master. This state is reported by the the host itself.
|
| networkIsolated |
A host is alive but is isolated from the management network.
See ClusterDasVmSettingsIsolationResponse for the criteria
used to determine whether a host is isolated.
|
| networkPartitionedFromMaster |
A slave host is alive and has management network connectivity, but
the management network has been partitioned. This state is reported
by masters that are in a partition other than the one containing the
slave host; the master in the slave's partition will report the slave state
as connectedToMaster.
|
| uninitializationError |
An error occurred when unconfiguring the Fault Domain Manager
running on a host. In order to clear this condition the host might
need to be reconnected to the cluster and reconfigured first.
This state is reported by vCenter
Server.
|
| uninitialized |
The Fault Domain Manager for the host has not yet been
initialized. Hence the host is not part of a vSphere HA
fault domain. This state is reported by vCenter Server or
by the host itself.
|


Before Change
// Creating multiple descriptors in parallel
from dscribe.utils import batch_create
molecule_lst = [water, methanol]
batch = batch_create(average_soap, molecule_lst, n_proc=1)
print(batch.shape)
After Change
print(soap_water.shape)
// Create output for multiple system
samples = [molecule("H2O"), molecule("NO2"), molecule("CO2")]
positions = [[0], [1, 2], [1, 2]]
coulomb_matrices = soap.create(samples, positions) // Serial
coulomb_matrices = soap.create(samples, positions, n_jobs=2) // Parallel
// Lets change the SOAP setup and see how features change
minimal_soap = SOAP(species=atomic_numbers, rcut=rcut, nmax=2, lmax=0)


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