Merge pull request #66 from TimMonko/measure_fix_tx_regex

update measure container and add a new test

src/napari_ndev/_measure_container.py

@@ -246,8 +246,10 @@ def _init_id_regex_container(self):
     def _init_tx_map_container(self):
         """Initialize the container for treatment map settings."""
         self._tx_map_container = Container(layout='vertical')
-        self._tx_id = LineEdit(
+        self._update_tx_id_choices_button = PushButton(label='Update Treatment ID Choices')
+        self._tx_id = ComboBox(
             label='Treatment ID',
+            choices=['id'],
             value=None,
             nullable=True,
             tooltip='Usually, the treatment ID is the well ID or a unique identifier for each sample'
@@ -265,7 +267,12 @@ def _init_tx_map_container(self):
         # TODO: Add example treatment regex result widget when example id string or id regex dict is changed
 
         self._tx_map_container.extend(
-            [self._tx_id, self._tx_n_well, self._tx_dict]
+            [
+                self._update_tx_id_choices_button,
+                self._tx_id,
+                self._tx_n_well,
+                self._tx_dict,
+            ]
         )
 
     def _init_grouping_container(self):
@@ -347,10 +354,20 @@ def _connect_events(self):
         self._image_directory.changed.connect(self._update_image_choices)
         self._label_directory.changed.connect(self._update_label_choices)
         self._region_directory.changed.connect(self._update_region_choices)
+        self._update_tx_id_choices_button.clicked.connect(self._update_tx_id_choices)
         self._measure_button.clicked.connect(self.batch_measure)
         self._measured_data_path.changed.connect(self._update_grouping_cols)
         self._group_measurements_button.clicked.connect(self.group_measurements)
 
+    def _update_tx_id_choices(self):
+        """Update the choices for treatment ID."""
+        id_regex_dict = self._safe_dict_eval(self._id_regex_dict.value)
+        if id_regex_dict is None:
+            return
+        # add the keys to a list which already contains 'id'
+        regex_choices = list(id_regex_dict.keys())
+        self._tx_id.choices = ['id'] + regex_choices
+
     def _update_grouping_cols(self):
         """Update the columns for grouping."""
         if self._measured_data_path.value is None:

src/napari_ndev/_tests/resources/Measure/.log.txt

@@ -0,0 +1,35 @@
+2024-09-21 10:52:17,855 -
+            Label Image: Labels: Morphology
+            Intensity Channels: ['Labels: DAPI Class']
+            Num. Files: 4
+            Label Directory: C:\Users\timmo\napari-ndev\src\napari_ndev\_tests\resources\Measure\Labels
+            Image Directory: None
+            Region Directory: None
+            Output Directory: C:\Users\timmo\napari-ndev\src\napari_ndev\_tests\resources\Measure
+            ID Example: 2024-08-07 25x 24HIC NCOA4 647 FT 568 PHALL 488 DAPI OBL_2_1_P4-A9.ome__0__Image:0
+            ID Regex Dict: {
+    'scene': r'(P\d{1,3}-\w+).ome',
+    'well': r'-(\w+).ome',
+    'HIC': r'(\d{1,3})HIC',
+    'date': r'(\d{4}-\d{2}-\d{2})',
+}
+
+            Tx ID: well
+            Tx N Well: 96
+            Tx Dict: {
+  'chelation':{
+    'Control': ['B1:C12'],
+    '50uM DFP': ['D1:E12'],
+    '100uM DFP': ['F1:G12'],
+    '100uM DFO': ['A1:A12', 'H1:H12'],
+  },
+}
+
+2024-09-21 10:52:17,858 - Processing file 2024-08-07 25x 24HIC NCOA4 647 FT 568 PHALL 488 DAPI OBL_2_1_P4-A9.ome.tiff
+2024-09-21 10:52:17,921 - Processing scene 0
+2024-09-21 10:52:18,082 - Processing file 2024-08-07 25x 24HIC NCOA4 647 FT 568 PHALL 488 DAPI OBL_56_55_P8-D9.ome.tiff
+2024-09-21 10:52:18,139 - Processing scene 0
+2024-09-21 10:52:18,303 - Processing file 2024-08-07 25x 48HIC NCOA4 647 FT 568 PHALL 488 DAPI OBL_36_35_P6-C9.ome.tiff
+2024-09-21 10:52:18,361 - Processing scene 0
+2024-09-21 10:52:18,520 - Processing file 2024-08-07 25x 72HIC NCOA4 647 FT 568 PHALL 488 DAPI OBL_22_21_P7-B9.ome.tiff
+2024-09-21 10:52:18,584 - Processing scene 0

src/napari_ndev/_tests/test_measure_container.py

@@ -140,6 +140,44 @@ def test_batch_measure_intensity(tmp_path):
     ]
 
 
+def test_batch_measure_with_regex(tmp_path):
+    container = MeasureContainer()
+    label_directory = pathlib.Path(
+        'src/napari_ndev/_tests/resources/Measure/Labels'
+    )
+    output_folder = tmp_path / 'Output'
+    output_folder.mkdir()
+
+    container._label_directory.value = label_directory
+    container._id_regex_dict.value = r"""
+        {
+            'scene': r'(P\d{1,3}-\w+).ome',
+            'well': r'-(\w+).ome',
+            'HIC': r'(\d{1,3})HIC',
+            'date': r'(\d{4}-\d{2}-\d{2})',
+        }
+    """
+    container._update_tx_id_choices_button.clicked()
+    assert container._tx_id.choices == (None, 'id','scene', 'well', 'HIC', 'date')
+
+    container._tx_id.value = 'well'
+    container._tx_n_well.value = 96
+    container._tx_dict.value = r"""
+        {
+            'chelation':{
+                'Control': ['B1:C12'],
+                '50uM DFP': ['D1:E12'],
+                '100uM DFP': ['F1:G12'],
+                '100uM DFO': ['A1:A12', 'H1:H12'],
+            },
+        }
+    """
+
+    df = container.batch_measure()
+    assert 'scene' in df.columns
+    assert 'well' in df.columns
+    assert 'chelation' in df.columns
+
 def test_group_measurements_no_agg_defaults():
     container = MeasureContainer()
     test_data_path = pathlib.Path(r'src/napari_ndev/_tests/resources/measure_props_Labels.csv')