Merge branch 'main' of https://github.com/winawerlab/nyu-annotate into main

Author: noahbenson

config/config.yaml

@@ -316,6 +316,58 @@ figures:
     cod: |
         ny.cortex_plot(target['flatmap'], color='cod', axes=axes, cmap='hot',
                        vmin=0, vmax=1)
+    # We also want to have thresholded versions of these plots.
+    polar_angle_thresh: |
+        ny.cortex_plot(target['flatmap'], color='polar_angle', axes=axes,
+                       mash=('cod', 0.1, 1), cmap='hot', vmin=0, vmax=1)
+    eccentricity_thresh: |
+        ny.cortex_plot(target['flatmap'], color='eccentricity', axes=axes,
+                       mash=('cod', 0.1, 1), cmap='hot', vmin=0, vmax=1)
     # The rest are PRF properties.
     _: |
         ny.cortex_plot(target['flatmap'], color=key, axes=axes)
+
+review: |
+  #from annotate import watershed_contours
+  #im = watershed_contours(annotations.values(), max_depth=1)
+  #axes.imshow(im, cmap='hsv', vmin=0, vmax=1.5*np.max(im))
+  import numpy as np
+  from matplotlib.pyplot import Polygon
+  # V1:
+  v1uvm = annotations['V1 UVM (ventral)']
+  v1lvm = annotations['V1 LVM (dorsal)']
+  v1per = annotations['V1 Periphery']
+  v1pol = Polygon(
+      np.vstack([v1uvm, v1per, np.flipud(v1lvm)]),
+      closed=True,
+      color='red',
+      alpha=0.5,
+      fill=True)
+  axes.add_patch(v1pol)
+  # V2:
+  v2uvm = annotations['V2 UVM (ventral)']
+  v2lvm = annotations['V2 LVM (dorsal)']
+  v2pev = annotations['V2 Ventral Periphery']
+  v2ped = annotations['V2 Dorsal Periphery']
+  v2pol = Polygon(
+      np.vstack(
+          [v2uvm, v2pev, np.flipud(v1uvm), v1lvm, v2ped, np.flipud(v2lvm)]),
+      closed=True,
+      color='cyan',
+      alpha=0.5,
+      fill=True)
+  axes.add_patch(v2pol)
+  # V3:
+  v3uvm = annotations['V3 UVM (ventral)']
+  v3lvm = annotations['V3 LVM (dorsal)']
+  v3pev = annotations['V3 Ventral Periphery']
+  v3ped = annotations['V3 Dorsal Periphery']
+  v3pol = Polygon(
+      np.vstack(
+          [v3uvm, v3pev, np.flipud(v2uvm), v2lvm, v3ped, np.flipud(v3lvm)]),
+      color='black',
+      alpha=0.5,
+      closed=True)
+  axes.add_patch(v3pol)
+  axes.axis('equal')
+  axes.axis('off')

src/annotate/__init__.py

@@ -18,7 +18,7 @@
 
 # Imports ######################################################################
 
-from ._util import (delay, ldict)
+from ._util import (delay, ldict, watershed_contours)
 from ._core import AnnotationTool
 
 

src/annotate/_config.py

@@ -511,6 +511,50 @@ def __init__(self, yaml, init, all_figures):
                                                       init)
         # Same these into the dictionary.
         self.update(res)
+class ReviewConfig:
+    """An object that stores the configuration of the review panel.
+
+    The `ReviewConfig` type stores information from the `review` section of the
+    `config.yaml` file for the `cortex-annotate` project. This section stores
+    only a function that generates the figure to plot in the `Review` tab of the
+    display panel. The review function requires the arguments `target`,
+    `annotations`, `figure`, and `axes`, and it must draw the desired graphics
+    on the given matplotlib axes. The `annotations` argument is a dictionary
+    whose keys are the annotation names and whose values are the drawn
+    annotation. Annotations may be missing if the user opens the review tab
+    before completing the annotations. If an error is raised from this function,
+    then the error message is printed to the display.
+    """
+    __slots__ = ('code', 'function', 'figsize', 'dpi')
+    @staticmethod
+    def _compile(code, initcfg):
+        return _compile_fn(
+            "target, annotations, figure, axes",
+            f"{code}\n",
+            initcfg)
+    def __init__(self, yaml, init):
+        if yaml is None:
+            self.code = None
+            self.function = None
+            self.figsize = None
+            self.dpi = None
+            return
+        elif isinstance(yaml, str):
+            yaml = {'function': yaml}
+        elif not isinstance(yaml, dict):
+            raise ConfigError(
+                "review",
+                "review section must contain a Python code string or a dict",
+                yaml)
+        self.code = yaml.get('function')
+        if self.code is None:
+            raise ConfigError(
+                "review",
+                "review section must contain the key function",
+                yaml)
+        self.figsize = yaml.get('figsize', (3,3))
+        self.dpi = yaml.get('dpi', 256)
+        self.function = ReviewConfig._compile(self.code, init)
 class Config:
     """The configuration object for the `cortex-annotate` project.
 
@@ -521,8 +565,9 @@ class Config:
     not recognized by `Config` are not parsed, but they are available in the
     `Config.yaml` member variable.
     """
-    __slots__ = ('config_path', 'yaml', 'display', 'init', 'targets', 'figures',
-                 'annotations', 'builtin_annotations', 'annotation_types')
+    __slots__ = (
+        'config_path', 'yaml', 'display', 'init', 'targets', 'figures',
+        'annotations', 'builtin_annotations', 'review', 'annotation_types')
     def __init__(self, config_path='/config/config.yaml'):
         self.config_path = config_path
         with open(config_path, 'rt') as f:
@@ -534,15 +579,20 @@ def __init__(self, config_path='/config/config.yaml'):
         # Parse the targets section.
         self.targets = TargetsConfig(self.yaml.get('targets', None), self.init)
         # Parse the annotations section.
-        self.annotations = AnnotationsConfig(self.yaml.get('annotations', None),
-                                             self.init)
+        self.annotations = AnnotationsConfig(
+            self.yaml.get('annotations', None),
+            self.init)
         # Parse the builtin_annotations section.
         self.builtin_annotations = BuiltinAnnotationsConfig(
             self.yaml.get('builtin_annotations', None),
             self.init)
         # Parse the figures section.
-        self.figures = FiguresConfig(self.yaml.get('figures', None), self.init,
-                                     self.annotations.all_figures)
+        self.figures = FiguresConfig(
+            self.yaml.get('figures', None),
+            self.init,
+            self.annotations.all_figures)
+        # Parse the review section.
+        self.review = ReviewConfig(self.yaml.get('review', None), self.init)
         # Make the annotation types dictionary.
         d = self.annotations.types.copy()
         d.update(self.builtin_annotations.types)

src/annotate/_control.py

@@ -333,11 +333,31 @@ def __init__(self, state,
         self.imagesize_slider = self._make_imagesize_slider(imagesize)
         self.selection_panel = SelectionPanel(state)
         self.style_panel = StylePanel(state)
+        self.review_button = ipw.Button(
+            description='Review',
+            button_style='',
+            tooltip='Review the annotations.')
         self.save_button = ipw.Button(
             description='Save',
             button_style='',
-            tooltip='Save all annotations and preferences.',
-            layout={'margin':"3% 33% 3% 33%", "width": "34%"})
+            tooltip='Save all annotations and preferences.')
+        self.edit_button = ipw.Button(
+            description='Edit',
+            button_style='',
+            tooltip='Continue editing annotation.')
+        if state.config.review.function is not None:
+            buttons = [self.review_button, self.save_button, self.edit_button]
+            self.review_button.disabled = False
+            self.save_button.disabled = True
+            self.edit_button.disabled = True
+            layout = {'margin':"3% 3% 3% 3%", "width": "94%"}
+        else:
+            buttons = [self.save_button]
+            self.review_button.disabled = True
+            self.save_button.disabled = False
+            self.edit_button.disabled = True
+            layout = {'margin':"3% 33% 3% 33%", "width": "34%"}
+        self.button_box = ipw.HBox(buttons, layout=layout)
         self.info_message = self._make_infomsg()
         hline = self._make_hline()
         self.vbox_children = [
@@ -348,7 +368,7 @@ def __init__(self, state,
             hline,
             self.style_panel,
             hline,
-            self.save_button,
+            self.button_box,
             hline,
             self.info_message]
         vbox_layout = {'width': '250px'}
@@ -433,10 +453,24 @@ def observe_imagesize(self, fn):
     def observe_save(self, fn):
         """Registers the argument to be called when the save button is clicked.
         
-        The function is called with a single argument, which is the save buttom
+        The function is called with a single argument, which is the save button
         instance.
         """
         self.save_button.on_click(fn)
+    def observe_review(self, fn):
+        """Registers the argument to be called when the save button is clicked.
+        
+        The function is called with a single argument, which is the review
+        button instance.
+        """
+        self.review_button.on_click(fn)
+    def observe_edit(self, fn):
+        """Registers the argument to be called when the edit button is clicked.
+        
+        The function is called with a single argument, which is the edit button
+        instance.
+        """
+        self.edit_button.on_click(fn)
     @property
     def target(self):
         """Compute the current target selection."""