Added more anisotropy handling + fix global in review (#14)

* Added more anisotropy handling + fix global in review

- Added to inference
- Added to crop
- Moved all anisotropy functions to AnisoWIdgets class
- Fixed logo for helper

- Removed global in review, now always opens in new window

- Added weights to gitignore (.pth)

* Update tox.ini

Test fix

* lint

black

* Test fix + napari hub quickstart

- Changed review test
- Wrote missing quickstart for napari-hub

* Trying to fix loose viewer in tests

* Test fix

Author: C-Achard

.gitignore

@@ -9,6 +9,7 @@ __pycache__/
 # unwanted results files
 *.tif
 napari_cellseg3d/_tests/res/*.csv
+*.pth
 
 # Distribution / packaging
 .Python

.napari/DESCRIPTION.md

@@ -68,9 +68,19 @@ make sure to mention this.
 If you know of researchers, groups or labs using your plugin, or if it has been cited
 anywhere, feel free to also include this information here.
 -->
-<!--
 ## Quickstart
 
+Install from pip with `pip install napari-cellseg3d`
+
+OR
+
+- Install napari from pip with `pip install "napari[all]"`,
+then from the “Plugins” menu within the napari application, select “Install/Uninstall Package(s)...”
+- Copy `napari-cellseg3d` and paste it where it says “Install by name/url…”
+- Click “Install”
+<!--
+
+
 This section should go through step-by-step examples of how your plugin should be used.
 Where your plugin provides multiple dock widgets or functions, you should split these
 out into separate subsections for easy browsing. Include screenshots and videos

README.md

@@ -66,7 +66,7 @@ If you encounter any problems, please [file an issue] along with a detailed desc
 To run tests locally:
 
 - Locally : run ``pytest`` in the plugin folder
-- Locally with coverage : In the plugin folder, run ``coverage run --source=src -m pytest`` then ``coverage.xml`` to generate a .xml coverage file.
+- Locally with coverage : In the plugin folder, run ``coverage run --source=napari_cellseg3d -m pytest`` then ``coverage xml`` to generate a .xml coverage file.
 - With tox : run ``tox`` in the plugin folder (will simulate tests with several python and OS configs, requires substantial storage space)
 
 ## Contributing

docs/res/logo/logo_alpha.png

@@ -5,20 +5,23 @@
 
 def test_launch_review(make_napari_viewer):
 
-    view = make_napari_viewer()
-    widget = rev.Reviewer(view)
+        view = make_napari_viewer()
+        widget = rev.Reviewer(view)
 
-    # widget.filetype_choice.setCurrentIndex(0)
+        # widget.filetype_choice.setCurrentIndex(0)
 
-    im_path = os.path.dirname(os.path.realpath(__file__)) + "/res/test.tif"
+        im_path = os.path.dirname(os.path.realpath(__file__)) + "/res/test.tif"
 
-    widget.image_path = im_path
-    widget.label_path = im_path
+        widget.image_path = im_path
+        widget.label_path = im_path
+
+        print(widget.image_path)
+        print(widget.label_path)
+        print(widget.as_folder)
+        print(widget.filetype)
+        widget.run_review()
+        widget._viewer.close()
+
+        assert widget._viewer is not None
 
-    print(widget.image_path)
-    print(widget.label_path)
-    print(widget.as_folder)
-    print(widget.filetype)
-    widget.run_review()
 
-    assert widget._viewer is not None

docs/res/logo/logo_background.png

@@ -41,7 +41,7 @@
 BOTT_AL = Qt.AlignmentFlag.AlignBottom
 """Alias for Qt.AlignmentFlag.AlignBottom, to use in addWidget"""
 ###############
-
+# colors
 dark_red = "#72071d"  # crimson red
 default_cyan = "#8dd3c7"  # turquoise cyan (default matplotlib line color under dark background context)
 napari_grey = "#262930"  # napari background color (grey)
@@ -95,7 +95,7 @@ def open_file_dialog(
         return filenames
 
 
-def make_label(name, parent=None):
+def make_label(name, parent=None):  # TODO update to child class
     """Creates a QLabel
 
     Args:
@@ -113,7 +113,7 @@ def make_label(name, parent=None):
 
 def make_scrollable(
     contained_layout, containing_widget, min_wh=None, max_wh=None, base_wh=None
-):
+):  # TODO convert to child class
     """Creates a QScrollArea and sets it up, then adds the contained_widget to it,
     and finally adds the scroll area in a layout and sets it to the contaning_widget
 
@@ -163,7 +163,7 @@ def make_n_spinboxes(
     parent=None,
     double=False,
     fixed=True,
-) -> Union[list, QWidget]:
+) -> Union[list, QWidget]:  # TODO: child class if possible ?
     """
 
     Args:
@@ -222,7 +222,7 @@ def add_to_group(title, widget, layout, L=7, T=20, R=7, B=11):
     layout.addWidget(group)
 
 
-def make_group(title, L=7, T=20, R=7, B=11, parent=None):
+def make_group(title, L=7, T=20, R=7, B=11, parent=None):  # TODO : child class
     """Creates a group widget and layout, with a header (`title`) and content margins for top/left/right/bottom `L, T, R, B` (in pixels)
     Group widget and layout returned will have a Fixed size policy.
 
@@ -246,7 +246,9 @@ def make_group(title, L=7, T=20, R=7, B=11, parent=None):
     return group, layout
 
 
-def make_container(L=0, T=0, R=1, B=11, vertical=True, parent=None):
+def make_container(
+    L=0, T=0, R=1, B=11, vertical=True, parent=None
+):  # TODO child class?
     """Creates a QWidget and a layout for the purpose of containing other modules, with a Fixed layout.
 
     Args:
@@ -276,7 +278,7 @@ def make_container(L=0, T=0, R=1, B=11, vertical=True, parent=None):
     return container_widget, container_layout
 
 
-def make_button(
+def make_button(  # TODO child class
     title: str = None,
     func: callable = None,
     parent: QWidget = None,
@@ -339,7 +341,7 @@ def __init__(
             self.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
 
 
-def make_combobox(
+def make_combobox(  # TODO child class
     entries=None,
     parent: QWidget = None,
     label: str = None,
@@ -405,7 +407,7 @@ def __init__(
             self.toggled.connect(func)
 
 
-def make_checkbox(
+def make_checkbox(  # TODO update calls to class
     title: str = None,
     func: callable = None,
     parent: QWidget = None,
@@ -508,9 +510,9 @@ def __init__(self, parent, default_x=1, default_y=1, default_z=1):
         self.box_widgets = make_n_spinboxes(
             n=3, min=1.0, max=1000, default=1, step=0.5, double=True
         )
-        self.box_widgets[0].setValue(default_x)  # TODO change default
-        self.box_widgets[1].setValue(default_y)  # TODO change default
-        self.box_widgets[2].setValue(default_z)  # TODO change default
+        self.box_widgets[0].setValue(default_x)
+        self.box_widgets[1].setValue(default_y)
+        self.box_widgets[2].setValue(default_z)
 
         for w in self.box_widgets:
             w.setSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
@@ -547,9 +549,48 @@ def build(self):
         add_widgets(self._layout, [self.checkbox, self.container])
         self.setLayout(self._layout)
 
-    def get_anisotropy_factors(self):
-        """Returns : the resolution in microns for each of the three dimensions"""
-        return [w.value() for w in self.box_widgets]
+    def get_anisotropy_resolution_xyz(self, as_factors=True):
+        """
+        Args :
+            as_factors: if True, returns zoom factors, otherwise returns the input resolution
+
+        Returns : the resolution in microns for each of the three dimensions. ZYX order suitable for napari scale"""
+
+        resolution = [w.value() for w in self.box_widgets]
+        if as_factors:
+            return self.anisotropy_zoom_factor(resolution)
+
+        return resolution
+
+    def get_anisotropy_resolution_zyx(self, as_factors=True):
+        """
+        Args :
+            as_factors: if True, returns zoom factors, otherwise returns the input resolution
+
+        Returns : the resolution in microns for each of the three dimensions. XYZ order suitable for MONAI"""
+        resolution = [w.value() for w in self.box_widgets]
+        if as_factors:
+            resolution = self.anisotropy_zoom_factor(resolution)
+
+        return [resolution[2], resolution[1], resolution[0]]
+
+    def anisotropy_zoom_factor(self, aniso_res):
+        """Computes a zoom factor to correct anisotropy, based on anisotropy resolutions
+
+            Args:
+                resolutions: array for resolution (float) in microns for each axis
+
+        Returns: an array with the corresponding zoom factors for each axis (all values divided by min)
+
+        """
+
+        base = min(aniso_res)
+        zoom_factors = [base / res for res in aniso_res]
+        return zoom_factors
+
+    def is_enabled(self):
+        """Returns : whether anisotropy correction has been enabled or not"""
+        return self.checkbox.isChecked()
 
 
 def open_url(url):

napari_cellseg3d/_tests/test_review.py

@@ -2,10 +2,12 @@
 from pathlib import Path
 
 import matplotlib.pyplot as plt
+import napari
 import numpy as np
 from magicgui import magicgui
-from matplotlib.backends.backend_qt5agg import \
-    FigureCanvasQTAgg as FigureCanvas
+from matplotlib.backends.backend_qt5agg import (
+    FigureCanvasQTAgg as FigureCanvas,
+)
 from matplotlib.figure import Figure
 from monai.transforms import Zoom
 from qtpy.QtWidgets import QSizePolicy
@@ -17,7 +19,6 @@
 
 
 def launch_review(
-    viewer,
     original,
     base,
     raw,
@@ -48,7 +49,6 @@ def launch_review(
       and determine whether it should be labeled or not.
 
     Args:
-        viewer (napari.viewer.Viewer): The viewer the widgets are to be displayed in
 
         original (dask.array.Array): The original images/volumes that have been labeled
 
@@ -68,12 +68,13 @@ def launch_review(
 
         zoom_factor (array(int)): zoom factors for each axis
 
-
+    Returns : list of all docked widgets
     """
     images_original = original
     base_label = base
 
-    view1 = viewer
+    view1 = napari.Viewer()
+    viewer = view1 #TODO fix duplicate name
 
     view1.scale_bar.visible = True
 
@@ -144,10 +145,6 @@ def launch_review(
     #     return labeled_c, labeled_sorted, nums
     #
     # worker = create_label()
-
-    layer = view1.layers[0]
-    layer1 = view1.layers[1]
-
     # if not as_folder:
     #     r_path = os.path.dirname(r_path)
 
@@ -324,3 +321,5 @@ def crop_volume_around_point(points, layer):
             -inferior_bound[2] : 100 - superior_bound[2],
         ] = crop_temp
         return cropped_volume
+
+    return view1, [file_widget, canvas, dmg]

napari_cellseg3d/interface.py

@@ -3,6 +3,7 @@
 
 import napari
 import torch
+
 # Qt
 from qtpy.QtWidgets import QLineEdit
 from qtpy.QtWidgets import QProgressBar

napari_cellseg3d/launch_review.py

@@ -2,6 +2,7 @@
 from __future__ import print_function
 
 import numpy as np
+
 # from skimage.measure import marching_cubes
 # from skimage.measure import mesh_surface_area
 from skimage.measure import label