add test data

Kapoorlabs-CAPED · Oct 8, 2023 · cd26d10 · cd26d10
1 parent 2d27038
commit cd26d10
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Showing 6 changed files with 17 additions and 78 deletions.
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = vollseg-napari-mtrack
-version = attr: vollseg-napari-mtrack._version.__version__
+version = attr: vollseg_napari_mtrack._version.__version__
 description = Segment kymographs of microtubules, actin filaments and perform Ransac based fits to compute dynamic instability parameters for individual kymographs and also in batch
 long_description = file: README.md
 long_description_content_type = text/markdown

diff --git a/src/vollseg_napari_mtrack/__init__.py b/src/vollseg_napari_mtrack/__init__.py
@@ -4,16 +4,13 @@
     __version__ = "unknown"
 
 from ._reader import napari_get_reader
-from ._sample_data import make_sample_data
+from ._sample_data import get_microtubule_test_data
 from ._temporal_plots import TemporalStatistics
 from ._widget import plugin_wrapper_mtrack
-from ._writer import write_multiple, write_single_image
 
 __all__ = (
     "napari_get_reader",
-    "write_single_image",
-    "write_multiple",
-    "make_sample_data",
+    "get_microtubule_test_data",
     "plugin_wrapper_mtrack",
     "MTrackTable",
     "TemporalStatistics",

diff --git a/src/vollseg_napari_mtrack/_sample_data.py b/src/vollseg_napari_mtrack/_sample_data.py
@@ -1,21 +1,9 @@
-"""
-This module is an example of a barebones sample data provider for napari.
+from ._reader import reader_function
+from vollseg import test_microtubule_kymographs
 
-It implements the "sample data" specification.
-see: https://napari.org/stable/plugins/guides.html?#sample-data
 
-Replace code below according to your needs.
-"""
-from __future__ import annotations
+def get_microtubule_test_data():
 
-import numpy
-
-
-def make_sample_data():
-    """Generates an image"""
-    # Return list of tuples
-    # [(data1, add_image_kwargs1), (data2, add_image_kwargs2)]
-    # Check the documentation for more information about the
-    # add_image_kwargs
-    # https://napari.org/stable/api/napari.Viewer.html#napari.Viewer.add_image
-    return [(numpy.random.rand(512, 512), {})]
+    extracted_folder = test_microtubule_kymographs()
+    image = reader_function(extracted_folder)[0][0]
+    return [(image, {"name": "microtubule_kymographs"})]
diff --git a/src/vollseg_napari_mtrack/_version.py b/src/vollseg_napari_mtrack/_version.py
@@ -1,3 +1,2 @@
-
-__version__ = version = '1.4.3'
-__version_tuple__ = version_tuple = (1, 4, 3)
+__version__ = version = "1.4.4"
+__version_tuple__ = version_tuple = (1, 4, 4)
diff --git a/src/vollseg_napari_mtrack/_writer.py b/src/vollseg_napari_mtrack/_writer.py
diff --git a/src/vollseg_napari_mtrack/napari.yaml b/src/vollseg_napari_mtrack/napari.yaml
@@ -5,14 +5,8 @@ contributions:
     - id: vollseg-napari-mtrack.get_reader
       python_name: vollseg_napari_mtrack._reader:napari_get_reader
       title: Open data with VollSeg Napari MTrack Plugin
-    - id: vollseg-napari-mtrack.write_multiple
-      python_name: vollseg_napari_mtrack._writer:write_multiple
-      title: Save multi-layer data with VollSeg Napari MTrack Plugin
-    - id: vollseg-napari-mtrack.write_single_image
-      python_name: vollseg_napari_mtrack._writer:write_single_image
-      title: Save image data with VollSeg Napari MTrack Plugin
-    - id: vollseg-napari-mtrack.make_sample_data
-      python_name: vollseg_napari_mtrack._sample_data:make_sample_data
+    - id: vollseg-napari-mtrack.get_microtubule_test_data
+      python_name: vollseg_napari_mtrack._sample_data:get_microtubule_test_data
       title: Load sample data from VollSeg Napari MTrack Plugin
     - id: vollseg-napari-mtrack.widget
       python_name: vollseg_napari_mtrack._widget:plugin_wrapper_mtrack
@@ -22,17 +16,11 @@ contributions:
     - command: vollseg-napari-mtrack.get_reader
       accepts_directories: true
       filename_patterns: []
-  writers:
-    - command: vollseg-napari-mtrack.write_multiple
-      layer_types: ['image*','labels*']
-      filename_extensions: []
-    - command: vollseg-napari-mtrack.write_single_image
-      layer_types: ['image']
-      filename_extensions: ['.tif']
+
   sample_data:
-    - command: vollseg-napari-mtrack.make_sample_data
-      display_name: VollSeg Napari MTrack Plugin
-      key: unique_id.1
+    - key: get_microtubule_test_data
+      display_name: Test Microtubule Kymographs
+      command: vollseg-napari-mtrack.get_microtubule_test_data
   widgets:
     - command: vollseg-napari-mtrack.widget
       display_name: MTrack