Merge 4cfba36 into 562536a

CONTRIBUTING.md

@@ -15,21 +15,21 @@ Before sending your pull requests, make sure you have followed this list.
 
 ### Contributing code
 
-If you have improvements to Caliban, please send us your pull requests! If you are new to the process, Github has a
+If you have improvements to DeepCell Label, please send us your pull requests! If you are new to the process, Github has a
 [how-to](https://help.github.com/articles/using-pull-requests/).
 
 If you want to contribute, start working through the codebase. Navigate to the
-[Github "issues" tab](https://github.com/vanvalenlab/caliban/issues) and start
+[Github "issues" tab](https://github.com/vanvalenlab/deepcell-label/issues) and start
 looking through interesting issues. If you are not sure of where to start, look for one of the smaller/easier issues here i.e.
-[issues with the "good first issue" label](https://github.com/vanvalenlab/caliban/labels/good%20first%20issue)
+[issues with the "good first issue" label](https://github.com/vanvalenlab/deepcell-label/labels/good%20first%20issue)
 and then take a look at the
-[issues with the "contributions welcome" label](https://github.com/vanvalenlab/caliban/labels/stat%3Acontributions%20welcome).
+[issues with the "contributions welcome" label](https://github.com/vanvalenlab/deepcell-label/labels/stat%3Acontributions%20welcome).
 These are issues that we believe are well suited for outside contributions. If you decide to start on an issue, leave a comment so that other people know that you're working on it. If you want to help out, but not alone, use the issue comment thread to coordinate.
 
 ### Contribution guidelines and standards
 
 Before sending your pull request for
-[review](https://github.com/vanvalenlab/caliban/pulls),
+[review](https://github.com/vanvalenlab/deepcell-label/pulls),
 make sure your changes are consistent with the guidelines and follow the
 DeepCell coding style.
 
@@ -40,8 +40,8 @@ DeepCell coding style.
     changes to lower the maintenance cost.
 *   Bug fixes also generally require unit tests, because the presence of bugs
     usually indicates insufficient test coverage.
-*   When you contribute a new feature to Caliban, the maintenance burden is
-    (by default) transferred to the Caliban team. This means that the benefit
+*   When you contribute a new feature to DeepCell Label, the maintenance burden is
+    (by default) transferred to the DeepCell Label team. This means that the benefit
     of the contribution must be compared against the cost of maintaining the
     feature.
 *   As every PR requires CI/CD testing, we discourage

README.md

@@ -73,9 +73,9 @@ Annotation mode focuses on using an adjustable brush to modify annotations on a
 
 *n* - change brush label to an unusued label, so that a new label can be created with a unique id. Can be used with conversion brush to overwrite existing label with unused label (follow conversion brush prompt).
 
-*p* - color picker (click on a label to change the brush value to it)
+*p* - color picker (click on a label to change the brush label to it)
 
-*r* - turn on "conversion brush" setting, which changes brush behavior so that one label value is overwritten with another label value. No other labels are affected, and conversion brush will not draw on background. After turning on conversion brush, click on cell labels as prompted to set brush values.
+*r* - turn on "conversion brush" setting, which changes brush behavior so that one label value is overwritten with another label value. No other labels are affected, and conversion brush will not draw on background. After turning on conversion brush, click on cell labels as prompted to set brush labels.
 
 *t* - threshold to predict annotations based on brightness. After turning this on, click and drag to draw a bounding box around the cell you wish to threshold. Make sure to include some background in the bounding box for accurate threshold predictions. Whatever was thresholded as foreground within the bounding box will be added to the annotation as a new cell with unique label.
 
@@ -88,7 +88,7 @@ Annotation mode focuses on using an adjustable brush to modify annotations on a
 
 **To pan in image:** Hold down the spacebar while clicking and dragging image to pan. Alternatively, the keys *home, page up, page down, and end* can be used to jump across the screen. Holding the shift key while using these pan buttons will result in a smaller jump; holding the control key will snap to the edge of the image.
 
-*h* - switch between highlighted mode and non-highlighted mode (highlight exists in label- and pixel-editing modes but is displayed differently; label-editing highlighting recolors solid label with red, pixel-editing highlighting adds white or red outline around label in image). Once highlight mode is on, use *[ (left bracket) / ] (right bracket)* to decrement/increment selected cell label number.
+*h* - switch between highlighted mode and non-highlighted mode (highlight exists in whole-label mode and paint mode but is displayed differently; label-editing highlighting recolors solid label with red, paint mode highlighting adds white or red outline around label in image). Once highlight mode is on, use *[ (left bracket) / ] (right bracket)* to decrement/increment selected cell label number.
 
 *shift+h* - switch between showing and hiding annotation masks in the pixel editor
 
@@ -106,7 +106,7 @@ Annotation mode focuses on using an adjustable brush to modify annotations on a
 
 *shift + ↓ / ↑* - cycle between colormaps for viewing raw images (does not apply to pixel editor)
 
-*e* - toggle annotation mode between pixel-editing and whole-label-editing (when nothing else selected)
+*e* - toggle annotation mode between paint mode and whole-label mode (when nothing else selected)
 
 *scroll wheel* - change image or annotation maximum brightness
 
@@ -132,9 +132,9 @@ To install one, you can go to http://realvnc.com to download a free VNC viewer.
 ### Build a Docker Container
 
 ```bash
-git clone https://github.com/vanvalenlab/caliban.git
-cd caliban
-docker build -t caliban .
+git clone https://github.com/vanvalenlab/deepcell-label.git
+cd deepcell-label
+docker build -t deepcell-label .
 ```
 ### Run the New Docker Image
 
@@ -143,7 +143,7 @@ docker run \
 -p 5900:5900 \
 -v $PWD/desktop:/usr/src/app/desktop  \
 --privileged \
-caliban:latest
+deepcell-label:latest
 ```
 This will launch a new Docker container and run Xvfb, Fluxbox, and a VNC server. To access the container’s display, point a VNC client to 127.0.0.1.
 

browser/README.md

@@ -115,9 +115,9 @@ Annotation mode focuses on using an adjustable brush to modify annotations on a
 
 *n* - change brush label to an unusued label, so that a new cell can be created with a unique id
 
-*p* - color picker (click on a label to change the brush value to it)
+*p* - color picker (click on a label to change the brush label to it)
 
-*r* - turn on "conversion brush" setting, which changes brush behavior so that one label value is overwritten with another label value. No other labels are affected, and conversion brush will not draw on background. After turning on conversion brush, click on cell labels as prompted to set brush values. (Eraser mode is automatically turned off when the conversion brush is set.)
+*r* - turn on "conversion brush" setting, which changes brush behavior so that one label value is overwritten with another label value. No other labels are affected, and conversion brush will not draw on background. After turning on conversion brush, click on cell labels as prompted to set brush labels. (Eraser mode is automatically turned off when the conversion brush is set.)
 
 *t* - threshold to predict annotations based on brightness. After turning this on, click and drag to draw a bounding box around the cell you wish to threshold. Make sure to include some background in the bounding box for accurate threshold predictions. Whatever was thresholded as foreground within the bounding box will be added to the annotation as a new cell with unique label.
 

browser/application.py

@@ -10,13 +10,15 @@
 from flask_cors import CORS
 import flask_monitoringdashboard as dashboard
 from flask_compress import Compress
+from flask_dropzone import Dropzone
 
 import config
 from blueprints import bp
 from models import db
 
 
 compress = Compress()  # pylint: disable=C0103
+dropzone = Dropzone()  # pylint: disable=C0103
 
 
 class ReverseProxied(object):
@@ -79,6 +81,7 @@ def create_app(**config_overrides):
     app.register_blueprint(bp)
 
     compress.init_app(app)
+    dropzone.init_app(app)
 
     # For flask monitoring dashboard
     if config.DASHBOARD_CONFIG:
@@ -87,7 +90,7 @@ def create_app(**config_overrides):
         def group_action():
             """Apply custom grouping for action endpoint"""
             from flask import request
-            if request.endpoint == 'caliban.action':
+            if request.endpoint == 'label.action':
                 return request.view_args['action_type']
 
         dashboard.config.group_by = group_action