Layout changes and refactoring (#10)

* Update .gitignore

* Grouped layout helpers

* Delete gui_elements.py

* Code refactoring

* Moved segment.py for now

* Revert to segment.py

* Implement segmentation methods as separate classes

* Add layout folder

* Update segment.py

* Enable button label alignment

* Region label paint is ndim by default

* Rename segmentation method folder and bugfixes

* Take over Adam's fixes and further bugfixes

* get rid of wildcard import

* Update segment.py

* Adding comments to trigger commit hooks

* Update analysis.py

* Reformatted code

* Reset constants (defaults)

Back to original values

* Re-integrated loading function for atlas layers and brainreg

Otherwise CI breaks.

* bugfix constant naming

* updated GUI tests. Left out add_surface_points() for now

add_surface_points() seems to work when workflow is followed in GUI but fails in CI. Need to investigate a bit.

* Make imio requirement

* Bugfixes, test changes

* Separate methods chooser panel from loader and add button styling

.gitignore

@@ -86,6 +86,9 @@ target/
 # pyenv
 .python-version
 
+# vscode
+.vscode
+
 # celery beat schedule file
 celerybeat-schedule
 
@@ -117,3 +120,4 @@ venv.bak/
 .idea/
 
 *.~lock.*
+*.zip

brainreg_segment/layout/gui_constants.py

@@ -0,0 +1,28 @@
+# Constants used throughout
+WINDOW_HEIGHT = 750
+WINDOW_WIDTH = 1500
+COLUMN_WIDTH = 150
+
+LOADING_PANEL_ALIGN = (
+    "left"  # Alignment of text in pushbuttons in loading panel
+)
+SEGM_METHODS_PANEL_ALIGN = (
+    "left"  # Alignment of text in pushbuttons in methods chooser panel
+)
+
+POINT_SIZE = 100
+SPLINE_SIZE = 50
+NUM_COLORS = 10
+BRUSH_SIZE = 250
+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/layout/gui_elements.py

@@ -0,0 +1,147 @@
+# GUI ELEMENTS
+# from napari.resources import build_icons # Contains .SVGPATH to all icons for napari
+
+from qtpy.QtWidgets import (
+    QDoubleSpinBox,
+    QPushButton,
+    QCheckBox,
+    QLabel,
+    QSpinBox,
+    QComboBox,
+)
+
+
+def add_combobox(
+    layout,
+    label,
+    items,
+    row,
+    column=0,
+    label_stack=False,
+    callback=None,
+    width=150,
+):
+    if label_stack:
+        combobox_row = row + 1
+        combobox_column = column
+    else:
+        combobox_row = row
+        combobox_column = column + 1
+    combobox = QComboBox()
+    combobox.addItems(items)
+    if callback:
+        combobox.currentIndexChanged.connect(callback)
+    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
+
+
+def add_button(
+    label,
+    layout,
+    connected_function,
+    row,
+    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)
+    button.clicked.connect(connected_function)
+    return button
+
+
+# def add_radiobutton(
+#     label,
+#     layout,
+#     connected_function,
+#     row,
+#     column,
+#     visibility=True,
+#     minimum_width=0,
+#     alignment="center",
+# ):
+#     button = QRadioButton(label)
+#     if alignment == "center":
+#         pass
+#     elif alignment == "left":
+#         button.setStyleSheet(
+#             "QRadioButton { text-align: left; padding: 0; spacing: 30px;}"
+#         )
+#     elif alignment == "right":
+#         button.setStyleSheet(
+#             "QRadioButton { text-align: right; padding: 0; spacing: 30px;}"
+#         )
+
+#     # Too change indicator button ... needs to dynamically retrieve icon from Napari.
+#     # Icons are saved as .svg files under napari.resources SVGPATH
+#     # "QRadioButton::indicator"
+#     # "{"
+#     # "width:16px;"
+#     # "height:16px;"
+#     # "}"
+#     # "QRadioButton::indicator::unchecked"
+#     # "{"
+#     # "image: url(build_icons.SVGPATH/visibility_off.svg);"
+#     # "}"
+#     # "QRadioButton::indicator::checked"
+#     # "{"
+#     # "image: url(/opt/miniconda3/envs/analysis/lib/python3.6/site-packages/napari/resources/icons/visibility.svg);"
+#     # "}"
+#     # )
+
+#     button.setVisible(visibility)
+#     button.setMinimumWidth(minimum_width)
+#     layout.addWidget(button, row, column)
+#     button.clicked.connect(connected_function)
+#     return button
+
+
+def add_checkbox(layout, default, label, row, column=0):
+    box = QCheckBox()
+    box.setChecked(default)
+    layout.addWidget(QLabel(label), row, column)
+    layout.addWidget(box, row, column + 1)
+    return box
+
+
+def add_float_box(
+    layout, default, minimum, maximum, label, step, row, column=0
+):
+    box = QDoubleSpinBox()
+    box.setMinimum(minimum)
+    box.setMaximum(maximum)
+    box.setValue(default)
+    box.setSingleStep(step)
+    layout.addWidget(QLabel(label), row, column)
+    layout.addWidget(box, row, column + 1)
+    return box
+
+
+def add_int_box(layout, default, minimum, maximum, label, row, column=0):
+    box = QSpinBox()
+    box.setMinimum(minimum)
+    box.setMaximum(maximum)
+    # Not always set if not after min & max
+    box.setValue(default)
+    layout.addWidget(QLabel(label), row, column)
+    layout.addWidget(box, row, column + 1)
+    return box

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