Merge 9ecd712 into 2174c87

.gitignore

@@ -86,6 +86,9 @@ target/
 # pyenv
 .python-version
 
+# vscode
+.vscode
+
 # celery beat schedule file
 celerybeat-schedule
 

brainreg_segment/layout/gui_constants.py

@@ -0,0 +1,22 @@
+# Constants used throughout
+WINDOW_HEIGHT = 750
+WINDOW_WIDTH = 1500
+COLUMN_WIDTH = 150
+
+
+POINT_SIZE = 5
+SPLINE_SIZE = 4
+NUM_COLORS = 10
+BRUSH_SIZE = 10
+SPLINE_POINTS_DEFAULT = 1000
+SPLINE_SMOOTHING_DEFAULT = 0.1
+FIT_DEGREE_DEFAULT = 3
+
+SUMMARISE_TRACK_DEFAULT = True
+ADD_SURFACE_POINT_DEFAULT = False
+CALCULATE_VOLUMES_DEFAULT = True
+SUMMARIZE_VOLUMES_DEFAULT = True
+
+TRACK_FILE_EXT = ".points"
+IMAGE_FILE_EXT = ".tiff"
+BOUNDARIES_STRING = "Boundaries"

brainreg_segment/gui_elements.py → brainreg_segment/layout/gui_elements.py

@@ -1,3 +1,4 @@
+# GUI ELEMENTS
 from qtpy.QtWidgets import (
     QDoubleSpinBox,
     QPushButton,
@@ -9,7 +10,14 @@
 
 
 def add_combobox(
-    layout, label, items, row, column=0, label_stack=False, callback=None
+    layout,
+    label,
+    items,
+    row,
+    column=0,
+    label_stack=False,
+    callback=None,
+    width=150,
 ):
     if label_stack:
         combobox_row = row + 1
@@ -21,8 +29,15 @@ def add_combobox(
     combobox.addItems(items)
     if callback:
         combobox.currentIndexChanged.connect(callback)
-    combobox_label = QLabel(label)
-    layout.addWidget(combobox_label, row, column)
+    combobox.setMaximumWidth = width
+
+    if label is not None:
+        combobox_label = QLabel(label)
+        combobox_label.setMaximumWidth = width
+        layout.addWidget(combobox_label, row, column)
+    else:
+        combobox_label = None
+
     layout.addWidget(combobox, combobox_row, combobox_column)
     return combobox, combobox_label
 
@@ -35,8 +50,16 @@ def add_button(
     column,
     visibility=True,
     minimum_width=0,
+    alignment="center",
 ):
     button = QPushButton(label)
+    if alignment == "center":
+        pass
+    elif alignment == "left":
+        button.setStyleSheet("QPushButton { text-align: left; }")
+    elif alignment == "right":
+        button.setStyleSheet("QPushButton { text-align: right; }")
+
     button.setVisible(visibility)
     button.setMinimumWidth(minimum_width)
     layout.addWidget(button, row, column)

brainreg_segment/layout/utils.py

@@ -0,0 +1,35 @@
+# Small layout utils
+from napari.viewer import Viewer
+
+
+def disable_napari_btns(viewer):
+    """
+    Disable some Napari functions to hide them from user interation
+    - Transpose TODO: Understand how to add this properly with space conventions
+    - Grid view
+    - Console
+    - New labels layer
+    - New points layer
+    - New shapes layer
+
+    """
+    viewer.window.qt_viewer.viewerButtons.transposeDimsButton.setVisible(False)
+    viewer.window.qt_viewer.viewerButtons.gridViewButton.setVisible(False)
+    viewer.window.qt_viewer.viewerButtons.consoleButton.setVisible(False)
+    viewer.window.qt_viewer.layerButtons.newLabelsButton.setVisible(False)
+    viewer.window.qt_viewer.layerButtons.newPointsButton.setVisible(False)
+    viewer.window.qt_viewer.layerButtons.newShapesButton.setVisible(False)
+
+
+def disable_napari_key_bindings():
+    """
+    Disable some default key bingings that are unused
+    """
+
+    @Viewer.bind_key("Control-G", overwrite=True)
+    def no_grid_mode_warning(self):
+        print("Grid mode is not supported")
+
+    @Viewer.bind_key("Control-T", overwrite=True)
+    def no_tranpose_warning(self):
+        print("Transposing is not supported")

brainreg_segment/regions/IO.py

@@ -1,4 +1,4 @@
-import tifffile
+import imio
 import numpy as np
 
 from pathlib import Path
@@ -120,7 +120,7 @@ def save_regions_to_file(
     name = label_layer.name
 
     filename = destination_directory / (name + image_extension)
-    tifffile.imsave(filename, data.astype(np.int16))
+    imio.to_tiff(data.astype(np.int16), filename)
 
 
 def export_regions_to_file(image, filename, voxel_size, ignore_empty=True):

brainreg_segment/regions/analysis.py

@@ -1,6 +1,7 @@
 import numpy as np
 import pandas as pd
 
+
 from napari.qt.threading import thread_worker
 from skimage.measure import regionprops_table
 

brainreg_segment/regions/layers.py

@@ -1,5 +1,4 @@
 import tifffile
-
 import numpy as np
 
 from glob import glob
@@ -28,6 +27,7 @@ def add_new_label_layer(
     """
     labels = np.empty_like(base_image)
     label_layer = viewer.add_labels(labels, num_colors=num_colors, name=name)
+    label_layer.n_dimensional = True
     label_layer.selected_label = selected_label
     label_layer.brush_size = brush_size
     return label_layer