Applied black formatter

docs/source/conf.py

@@ -12,14 +12,15 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../../'))
+
+sys.path.insert(0, os.path.abspath("../../"))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'snub'
-copyright = '2022, Caleb Weinreb'
-author = 'Caleb Weinreb'
+project = "snub"
+copyright = "2022, Caleb Weinreb"
+author = "Caleb Weinreb"
 
 
 # -- General configuration ---------------------------------------------------
@@ -28,16 +29,17 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-	'sphinx.ext.autodoc',
-	'sphinx.ext.napoleon',
-	'sphinx.ext.autosummary',
-	'sphinx.ext.viewcode',
-	'sphinx.ext.coverage',
-	'sphinx.ext.autosectionlabel']
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinx.ext.autosectionlabel",
+]
 
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -50,16 +52,15 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-html_favicon = '../media/favicon.png'
+html_static_path = ["_static"]
 
-def setup(app):
-    app.add_css_file('css/custom.css')  # may also be an URL
+html_favicon = "../media/favicon.png"
 
 
+def setup(app):
+    app.add_css_file("css/custom.css")  # may also be an URL

snub/__main__.py

@@ -1,4 +1,4 @@
 from snub.gui.main import run
 
-if __name__ == '__main__':
-    run()
+if __name__ == "__main__":
+    run()

snub/gui/__init__.py

@@ -1,4 +1,4 @@
 from . import panels
 from . import stacks
 from . import tracks
-from . import main
+from . import main

snub/gui/panels/roi.py

@@ -19,129 +19,179 @@
 
 
 def _roi_contours(rois, dims, threshold_max_ratio=0.2, blur_kernel=2):
-    rois = np.array(rois.todense()).reshape(rois.shape[0],*dims)
+    rois = np.array(rois.todense()).reshape(rois.shape[0], *dims)
     contour_coordinates = []
     for roi in rois:
-        roi_blur = cv2.GaussianBlur(roi,(11,11),blur_kernel)
-        roi_mask = roi_blur > roi_blur.max()*threshold_max_ratio
-        xy = cv2.findContours(roi_mask.astype(np.uint8), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)[0][0].squeeze()
-        contour_coordinates.append(np.vstack((xy,xy[:1])))
+        roi_blur = cv2.GaussianBlur(roi, (11, 11), blur_kernel)
+        roi_mask = roi_blur > roi_blur.max() * threshold_max_ratio
+        xy = cv2.findContours(
+            roi_mask.astype(np.uint8), cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE
+        )[0][0].squeeze()
+        contour_coordinates.append(np.vstack((xy, xy[:1])))
     return contour_coordinates
 
 
 class ROIPanel(Panel, HeaderMixin):
     eps = 1e-10
 
-    def __init__(self, config, rois_path=None, labels_path=None, timestamps_path=None,
-                 dimensions=None, video_paths=None, contour_colors={}, linewidth=3, 
-                 initial_selected_rois=[], vmin=0, vmax=1, colormap='viridis', **kwargs):
-
+    def __init__(
+        self,
+        config,
+        rois_path=None,
+        labels_path=None,
+        timestamps_path=None,
+        dimensions=None,
+        video_paths=None,
+        contour_colors={},
+        linewidth=3,
+        initial_selected_rois=[],
+        vmin=0,
+        vmax=1,
+        colormap="viridis",
+        **kwargs
+    ):
         super().__init__(config, **kwargs)
 
         self.linewidth = linewidth
         self.colormap = colormap
-        self.vmin,self.vmax = vmin,vmax
+        self.vmin, self.vmax = vmin, vmax
         self.dims = dimensions
         self.current_frame_index = None
         self.is_visible = True
 
-        self.rois = load_npz(os.path.join(config['project_directory'],rois_path))
-        self.timestamps = np.load(os.path.join(config['project_directory'],timestamps_path))
+        self.rois = load_npz(os.path.join(config["project_directory"], rois_path))
+        self.timestamps = np.load(
+            os.path.join(config["project_directory"], timestamps_path)
+        )
 
-        if labels_path is None: self.labels = [str(i) for i in range(self.rois.shape[0])]
-        else: self.labels = open(os.path.join(config['project_directory'],labels_path),'r').read().split('\n')
+        if labels_path is None:
+            self.labels = [str(i) for i in range(self.rois.shape[0])]
+        else:
+            self.labels = (
+                open(os.path.join(config["project_directory"], labels_path), "r")
+                .read()
+                .split("\n")
+            )
 
         self.adjust_colormap_dialog = AdjustColormapDialog(self, self.vmin, self.vmax)
         self.adjust_colormap_dialog.new_range.connect(self.update_colormap_range)
 
-        self.canvas = SceneCanvas(self, keys='interactive', show=True)
+        self.canvas = SceneCanvas(self, keys="interactive", show=True)
         self.canvas.events.mouse_release.connect(self.mouse_release)
-        self.viewbox = self.canvas.central_widget.add_grid().add_view(row=0, col=0, camera='panzoom')
-        self.viewbox.camera.set_range(x=(0,self.dims[1]), y=(0,self.dims[0]), margin=0)
-        self.viewbox.camera.aspect=1
+        self.viewbox = self.canvas.central_widget.add_grid().add_view(
+            row=0, col=0, camera="panzoom"
+        )
+        self.viewbox.camera.set_range(
+            x=(0, self.dims[1]), y=(0, self.dims[0]), margin=0
+        )
+        self.viewbox.camera.aspect = 1
 
         self.contours = {}
-        for label,coordinates in zip(self.labels, _roi_contours(self.rois, self.dims)):
-            color = contour_colors[label] if label in contour_colors else _random_color()
-            self.contours[label] = Line(coordinates, color=np.array(color)/255, 
-                width=self.linewidth, connect='strip', parent=None)
-
-        self.vids = {name : VideoReader(
-            os.path.join(config['project_directory'],video_path)
-            ) for name,video_path in video_paths.items()}
+        for label, coordinates in zip(self.labels, _roi_contours(self.rois, self.dims)):
+            color = (
+                contour_colors[label] if label in contour_colors else _random_color()
+            )
+            self.contours[label] = Line(
+                coordinates,
+                color=np.array(color) / 255,
+                width=self.linewidth,
+                connect="strip",
+                parent=None,
+            )
+
+        self.vids = {
+            name: VideoReader(os.path.join(config["project_directory"], video_path))
+            for name, video_path in video_paths.items()
+        }
 
         self.dropDown = QComboBox()
         self.dropDown.addItems(list(video_paths.keys())[::-1])
         self.dropDown.activated.connect(self.update_image)
 
-        self.image = Image(np.zeros(self.dims, dtype=np.float32), 
-            cmap=colormap, parent=self.viewbox.scene, clim=(0,1))
-        self.update_current_time(config['init_current_time'])
+        self.image = Image(
+            np.zeros(self.dims, dtype=np.float32),
+            cmap=colormap,
+            parent=self.viewbox.scene,
+            clim=(0, 1),
+        )
+        self.update_current_time(config["init_current_time"])
         self.initUI(**kwargs)
 
     def initUI(self, **kwargs):
         super().initUI(**kwargs)
         self.layout.addWidget(self.dropDown)
         self.layout.addWidget(self.canvas.native)
         self.image.order = 1
-        for c in self.contours.values(): c.order=0
-        self.dropDown.setStyleSheet("""
+        for c in self.contours.values():
+            c.order = 0
+        self.dropDown.setStyleSheet(
+            """
             QComboBox::item { color: white; background-color : #3E3E3E;}
-            QComboBox::item:selected { background-color: #999999;} """)
+            QComboBox::item:selected { background-color: #999999;} """
+        )
 
     def update_visible_contours(self, visible_contours):
-        for l,c in self.contours.items():
+        for l, c in self.contours.items():
             if l in visible_contours:
                 c.parent = self.viewbox.scene
-            else: c.parent = None
+            else:
+                c.parent = None
 
     def update_current_time(self, t):
-        self.current_frame_index = min(self.timestamps.searchsorted(t), len(self.timestamps)-1)
-        if self.is_visible: self.update_image()
+        self.current_frame_index = min(
+            self.timestamps.searchsorted(t), len(self.timestamps) - 1
+        )
+        if self.is_visible:
+            self.update_image()
 
     def toggle_visiblity(self, *args):
         super().toggle_visiblity(*args)
-        if self.is_visible: self.update_image()
+        if self.is_visible:
+            self.update_image()
 
     def update_image(self):
         name = self.dropDown.currentText()
-        if self.current_frame_index is None: x = np.zeros(self.dims)
-        else: x = self.vids[name][self.current_frame_index][:,:,0]/255
-        image = (np.clip(x, self.vmin, self.vmax)-self.vmin)/(self.vmax-self.vmin)
+        if self.current_frame_index is None:
+            x = np.zeros(self.dims)
+        else:
+            x = self.vids[name][self.current_frame_index][:, :, 0] / 255
+        image = (np.clip(x, self.vmin, self.vmax) - self.vmin) / (self.vmax - self.vmin)
         self.image.set_data(image.astype(np.float32))
         self.canvas.update()
 
     def update_colormap_range(self, vmin, vmax):
-        self.vmin,self.vmax = vmin,vmax
+        self.vmin, self.vmax = vmin, vmax
         self.update_image()
 
     def show_adjust_colormap_dialog(self):
         self.adjust_colormap_dialog.show()
 
     def mouse_release(self, event):
-        if event.button == 2: self.context_menu(event)
+        if event.button == 2:
+            self.context_menu(event)
 
     def context_menu(self, event):
         contextMenu = QMenu(self)
-        def add_menu_item(name, slot, item_type='label'):
+
+        def add_menu_item(name, slot, item_type="label"):
             action = QWidgetAction(self)
-            if item_type=='checkbox': 
+            if item_type == "checkbox":
                 widget = QCheckBox(name)
                 widget.stateChanged.connect(slot)
-            elif item_type=='label': 
+            elif item_type == "label":
                 widget = QLabel(name)
                 action.triggered.connect(slot)
             action.setDefaultWidget(widget)
-            contextMenu.addAction(action)  
+            contextMenu.addAction(action)
             return widget
 
         # click to show adjust colormap range dialog
-        label = add_menu_item('Adjust colormap range',self.show_adjust_colormap_dialog)
+        label = add_menu_item("Adjust colormap range", self.show_adjust_colormap_dialog)
 
-        contextMenu.setStyleSheet("""
+        contextMenu.setStyleSheet(
+            """
             QMenu::item, QLabel, QCheckBox { background-color : #3E3E3E; padding: 5px 6px 5px 6px;}
             QMenu::item:selected, QLabel:hover, QCheckBox:hover { background-color: #999999;}
-            QMenu::separator { background-color: rgb(20,20,20);} """)
+            QMenu::separator { background-color: rgb(20,20,20);} """
+        )
         action = contextMenu.exec_(event.native.globalPos())
-
-