Merge pull request haesleinhuepf#21 from haesleinhuepf/load_csv

added function for loading CSV files into label layer properties

napari_skimage_regionprops/__init__.py

@@ -1,15 +1,16 @@
 from ._table import add_table, get_table, TableWidget
 from ._regionprops import regionprops, regionprops_table, regionprops_table_all_frames
 from ._parametric_images import visualize_measurement_on_labels
+from napari_plugin_engine import napari_hook_implementation
+from ._load_csv import load_csv
+
 try:
     from ._version import version as __version__
 except ImportError:
     __version__ = "0.4.1"
 
-from napari_plugin_engine import napari_hook_implementation
-
 
 @napari_hook_implementation
 def napari_experimental_provide_function():
-    return [regionprops_table, visualize_measurement_on_labels]
+    return [regionprops_table, visualize_measurement_on_labels, load_csv]
 

napari_skimage_regionprops/_load_csv.py

@@ -0,0 +1,29 @@
+import napari
+import numpy as np
+from napari_tools_menu import register_function
+
+@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):
+    """Save contents of a CSV file into a given layer's properties"""
+    import pandas as pd
+    # load region properties from csv file
+    reg_props = pd.read_csv(csv_filename)
+    try:
+        edited_reg_props = reg_props.drop(["Unnamed: 0"], axis=1)
+    except KeyError:
+        edited_reg_props = reg_props
+
+    if "label" not in edited_reg_props.keys().tolist():
+        label_column = pd.DataFrame(
+            {"label": np.array(range(1, (len(edited_reg_props) + 1)))}
+        )
+        edited_reg_props = pd.concat([label_column, edited_reg_props], axis=1)
+
+    if hasattr(labels_layer, "properties"):
+        labels_layer.properties = edited_reg_props
+    if hasattr(labels_layer, "features"):
+        labels_layer.features = edited_reg_props
+
+    if viewer is not None:
+        from ._table import add_table
+        add_table(labels_layer, viewer)

napari_skimage_regionprops/_tests/test_function.py

@@ -81,6 +81,14 @@ def test_regionprops(make_napari_viewer):
     table_widget.append_content(fake_area)
     assert 'Double area' in table_widget.get_content().keys()
 
+    # save table to disk
+    import pandas as pd
+    pd.DataFrame(labels_layer.properties).to_csv("test.csv")
+    from napari_skimage_regionprops import load_csv
+    load_csv("test.csv", labels_layer)
+    load_csv("test.csv", labels_layer, viewer)
+
+
     # empty table
     table_widget.set_content(None)
     table_widget.update_content()