Merge pull request #49 from haesleinhuepf/dev

Dev

README.md

@@ -84,9 +84,9 @@ The user can select categories of features for feature extraction in the user in
   * extent
   * feret_diameter_max
   * local_centroid
-  * roundness as defined for 2D labels [by ImageJ](https://imagej.nih.gov/ij/docs/menus/analyze.html)
-  * circularity as defined for 2D labels  [by ImageJ](https://imagej.nih.gov/ij/docs/menus/analyze.html)
-  * aspect_ratio as defined for 2D labels [by ImageJ](https://imagej.nih.gov/ij/docs/menus/analyze.html)
+  * roundness as defined for 2D labels [by ImageJ](https://imagej.nih.gov/ij/docs/menus/analyze.html#set)
+  * circularity as defined for 2D labels  [by ImageJ](https://imagej.nih.gov/ij/docs/menus/analyze.html#set)
+  * aspect_ratio as defined for 2D labels [by ImageJ](https://imagej.nih.gov/ij/docs/menus/analyze.html#set)
 * position:
   * centroid
   * bbox

napari_skimage_regionprops/__init__.py

@@ -8,7 +8,7 @@
 try:
     from ._version import version as __version__
 except ImportError:
-    __version__ = "0.7.0"
+    __version__ = "0.8.0"
 
 
 @napari_hook_implementation

napari_skimage_regionprops/_all_frames.py

@@ -1,5 +1,3 @@
-
-import napari
 from toolz import curry
 from typing import Callable
 from functools import wraps
@@ -8,6 +6,12 @@
 import pandas as pd
 from ._utilities import isimage
 
+try:
+    import napari
+except ModuleNotFoundError as e:
+    import warnings
+    warnings.warn(str(e))
+
 @curry
 def analyze_all_frames(function: Callable) -> Callable:
     from napari_workflows._workflow import _get_layer_from_data

napari_skimage_regionprops/_load_csv.py

@@ -1,9 +1,15 @@
-import napari
 import numpy as np
 from napari_tools_menu import register_function
 
+try:
+    import napari
+except ModuleNotFoundError as e:
+    import warnings
+    warnings.warn(str(e))
+
+
 @register_function(menu="Measurement > Load from CSV (nsr)")
-def load_csv(csv_filename:"magicgui.types.PathLike", labels_layer:napari.layers.Labels, viewer:napari.Viewer=None):
+def load_csv(csv_filename:"magicgui.types.PathLike", labels_layer: "napari.layers.Labels", viewer: "napari.Viewer" = None):
     """Save contents of a CSV file into a given layer's properties"""
     import pandas as pd
     # load region properties from csv file

napari_skimage_regionprops/_regionprops.py

@@ -2,13 +2,16 @@
 
 import numpy as np
 import pandas
-from napari import Viewer
+try:
+    import napari
+except ModuleNotFoundError as e:
+    warnings.warn(str(e))
+
 from napari_tools_menu import register_function
-import napari
 import math
 from ._all_frames import analyze_all_frames
 
-def regionprops(image_layer : napari.layers.Layer, labels_layer: napari.layers.Labels, size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False, napari_viewer : Viewer = None):
+def regionprops(image_layer: "napari.layers.Layer", labels_layer: "napari.layers.Labels", size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False, napari_viewer : "napari.Viewer" = None):
     warnings.warn("napari_skimage_regionprops.regionprops is deprecated. Use regionprops_table instead.")
     image_data = None
     if image_layer is not None:
@@ -17,7 +20,7 @@ def regionprops(image_layer : napari.layers.Layer, labels_layer: napari.layers.L
     regionprops_table(image_data, labels_layer.data, size, intensity, perimeter, shape, position, moments, napari_viewer)
 
 @register_function(menu="Measurement tables > Regionprops (scikit-image, nsr)")
-def regionprops_table(image : napari.types.ImageData, labels: napari.types.LabelsData, size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False, napari_viewer : Viewer = None) -> "pandas.DataFrame":
+def regionprops_table(image: "napari.types.ImageData", labels: "napari.types.LabelsData", size : bool = True, intensity : bool = True, perimeter : bool = False, shape : bool = False, position : bool = False, moments : bool = False, napari_viewer : "napari.Viewer" = None) -> "pandas.DataFrame":
     """
     Adds a table widget to a given napari viewer with quantitative analysis results derived from an image-label pair.
     """

napari_skimage_regionprops/_table.py

@@ -1,9 +1,14 @@
-import time
+try:
+    import napari
+    from qtpy.QtCore import QTimer
+    from qtpy.QtWidgets import QTableWidget, QHBoxLayout, QTableWidgetItem, QWidget, QGridLayout, QPushButton, QFileDialog
+except ModuleNotFoundError as e:
+    import warnings
+    warnings.warn(str(e))
+    class QWidget:
+        pass
 
-import napari
 from pandas import DataFrame
-from qtpy.QtCore import QTimer
-from qtpy.QtWidgets import QTableWidget, QHBoxLayout, QTableWidgetItem, QWidget, QGridLayout, QPushButton, QFileDialog
 from napari_tools_menu import register_function
 
 import pandas as pd
@@ -16,7 +21,7 @@ class TableWidget(QWidget):
     The table widget represents a table inside napari.
     Tables are just views on `properties` of `layers`.
     """
-    def __init__(self, layer: napari.layers.Layer, viewer:napari.Viewer = None):
+    def __init__(self, layer: "napari.layers.Layer", viewer: "napari.Viewer" = None):
         super().__init__()
 
         self._layer = layer
@@ -234,7 +239,7 @@ def append_content(self, table: Union[dict, DataFrame], how: str = 'outer'):
 
 
 @register_function(menu="Measurement > Show table (nsr)")
-def add_table(labels_layer: napari.layers.Layer, viewer:napari.Viewer) -> TableWidget:
+def add_table(labels_layer: "napari.layers.Layer", viewer: "napari.Viewer") -> TableWidget:
     """
     Add a table to a viewer and return the table widget. The table will show the `properties` of the given layer.
     """
@@ -250,7 +255,7 @@ def add_table(labels_layer: napari.layers.Layer, viewer:napari.Viewer) -> TableW
 
     return dock_widget
 
-def get_table(labels_layer: napari.layers.Layer, viewer:napari.Viewer) -> TableWidget:
+def get_table(labels_layer: "napari.layers.Layer", viewer: "napari.Viewer") -> TableWidget:
     """
     Searches inside a viewer for a given table and returns it. If it cannot find it,
     it will return None.
@@ -273,4 +278,4 @@ def _determine_frame_column(table):
     for c in candidates:
         if c in table.keys():
             return c
-    return None
+    return None

napari_skimage_regionprops/_utilities.py

@@ -1,18 +1,25 @@
 import numpy as np
-from napari_plugin_engine import napari_hook_implementation
-from napari.types import ImageData
-from napari import Viewer
+try:
+    from napari_plugin_engine import napari_hook_implementation
+    from napari.types import ImageData
+    import napari
+    from napari.layers import Image, Labels, Layer
+    from typing_extensions import Annotated
+    LayerInput = Annotated[Layer, {"label": "Image"}]
+except ModuleNotFoundError as e:
+    import warnings
+    warnings.warn(str(e))
+    LayerInput = None
+
 from napari_tools_menu import register_function
-from typing_extensions import Annotated
-from napari.layers import Image, Labels, Layer
-LayerInput = Annotated[Layer, {"label": "Image"}]
+
 
 @napari_hook_implementation
 def napari_experimental_provide_function():
     return [duplicate_current_frame]
 
 @register_function(menu="Utilities > Duplicate current timepoint (nsr)")
-def duplicate_current_frame(layer : LayerInput, napari_viewer : Viewer, axis : int = 0) -> Layer:
+def duplicate_current_frame(layer : LayerInput, napari_viewer: "napari.Viewer", axis : int = 0) -> "napari.layers.Layer":
     image = layer.data
     current_dim_value = napari_viewer.dims.current_step[axis]
     new_image = np.take(image, current_dim_value, axis)

requirements.txt

@@ -3,6 +3,6 @@ numpy
 scikit-image
 napari
 pandas
-napari-tools-menu>=0.1.11
+napari-tools-menu>=0.1.18
 napari-workflows
 imageio!=2.22.1

setup.py

@@ -36,7 +36,7 @@ def read(fname):
     packages=find_packages(),
     python_requires='>=3.8',
     install_requires=requirements,
-    version='0.7.0',
+    version='0.8.0',
     #use_scm_version=use_scm,
     setup_requires=['setuptools_scm'],
     classifiers=[