Merge 303e4f1 into 2a3ae44

ark/phenotyping/cell_cluster_utils.py

@@ -9,7 +9,7 @@
 import scipy.stats as stats
 
 from ark.analysis import visualize
-from ark.utils import misc_utils
+from ark.utils import misc_utils, io_utils
 
 
 def compute_cell_cluster_count_avg(cell_cluster_path, pixel_cluster_col_prefix,
@@ -96,10 +96,7 @@ def compute_cell_cluster_channel_avg(fovs, channels, base_dir,
     """
 
     # verify the cell table actually exists
-    if not os.path.exists(os.path.join(base_dir, weighted_cell_channel_name)):
-        raise FileNotFoundError(
-            "Weighted cell table %s not found in %s" % (weighted_cell_channel_name, base_dir)
-        )
+    io_utils.validate_paths(os.path.join(base_dir, weighted_cell_channel_name))
 
     # verify the cell cluster col specified is valid
     misc_utils.verify_in_list(
@@ -445,15 +442,8 @@ def train_cell_som(fovs, channels, base_dir, pixel_data_dir, cell_table_path,
     cluster_counts_norm_path = os.path.join(base_dir, cluster_counts_norm_name)
     weights_path = os.path.join(base_dir, weights_name)
 
-    # if the cell table path does not exist
-    if not os.path.exists(cell_table_path):
-        raise FileNotFoundError('Cell table path %s does not exist' %
-                                cell_table_path)
-
-    # if the pixel data with the SOM and meta labels path does not exist
-    if not os.path.exists(pixel_data_path):
-        raise FileNotFoundError('Pixel data dir %s does not exist in base_dir %s' %
-                                (pixel_data_path, base_dir))
+    # check the cell table path and pixel data path exist
+    io_utils.validate_paths([cell_table_path, pixel_data_path])
 
     # verify the cluster_col provided is valid
     misc_utils.verify_in_list(
@@ -550,17 +540,8 @@ def cluster_cells(base_dir, cluster_counts_norm_name='cluster_counts_norm.feathe
     weights_path = os.path.join(base_dir, weights_name)
     cell_data_path = os.path.join(base_dir, cell_data_name)
 
-    # if the path to the normalized pixel cluster counts per cell doesn't exist
-    if not os.path.exists(cluster_counts_norm_path):
-        raise FileNotFoundError(
-            'Normalized pixel cluster counts per cell file %s does not exist in base_dir %s' %
-            (cluster_counts_norm_name, base_dir)
-        )
-
-    # if the path to the weights file does not exist
-    if not os.path.exists(weights_path):
-        raise FileNotFoundError('Weights file %s does not exist in base_dir %s' %
-                                (weights_name, base_dir))
+    # check the path to the normalized pixel cluster counts per cell and weights file exists
+    io_utils.validate_paths([cluster_counts_norm_path, weights_path])
 
     # verify the pixel_cluster_col_prefix provided is valid
     misc_utils.verify_in_list(
@@ -678,26 +659,8 @@ def cell_consensus_cluster(fovs, channels, base_dir, pixel_cluster_col, max_k=20
     weighted_channel_path = os.path.join(base_dir, weighted_cell_channel_name)
     clust_to_meta_path = os.path.join(base_dir, clust_to_meta_name)
 
-    # if the path to the SOM clustered data doesn't exist
-    if not os.path.exists(cell_data_path):
-        raise FileNotFoundError(
-            'Cell data file %s does not exist in base_dir %s' %
-            (cell_data_name, base_dir)
-        )
-
-    # if the path to the average pixel cluster counts per cell cluster doesn't exist
-    if not os.path.exists(som_cluster_counts_avg_path):
-        raise FileNotFoundError(
-            'Average pix clust count per cell SOM cluster file %s does not exist in base_dir %s' %
-            (cell_som_cluster_count_avgs_name, base_dir)
-        )
-
-    # if the path to the weighted channel data doesn't exist
-    if not os.path.exists(weighted_channel_path):
-        raise FileNotFoundError(
-            'Weighted channel table %s does not exist in base_dir %s' %
-            (weighted_cell_channel_name, base_dir)
-        )
+    # check paths
+    io_utils.validate_paths([cell_data_path, som_cluster_counts_avg_path, weighted_channel_path])
 
     # verify the pixel_cluster_col provided is valid
     misc_utils.verify_in_list(
@@ -866,41 +829,10 @@ def apply_cell_meta_cluster_remapping(fovs, channels, base_dir, cell_consensus_n
     meta_cluster_channel_avgs_path = os.path.join(base_dir, cell_meta_cluster_channel_avg_name)
 
     # file path validation
-    if not os.path.exists(cell_consensus_path):
-        raise FileNotFoundError('Cell consensus file %s does not exist in base_dir %s' %
-                                (cell_consensus_name, base_dir))
-
-    if not os.path.exists(cell_remapped_path):
-        raise FileNotFoundError('Cell remapping file %s does not exist in base_dir %s' %
-                                (cell_remapped_name, base_dir))
-
-    if not os.path.exists(som_cluster_counts_avgs_path):
-        raise FileNotFoundError(
-            'Average pix clust count per cell SOM cluster file %s does not exist in base_dir %s' %
-            (cell_som_cluster_count_avgs_name, base_dir)
-        )
-
-    if not os.path.exists(meta_cluster_counts_avgs_path):
-        raise FileNotFoundError(
-            'Average pix clust count per cell meta cluster file %s does not exist in base_dir %s' %
-            (cell_meta_cluster_count_avgs_name, base_dir)
-        )
-
-    if not os.path.exists(weighted_channel_path):
-        raise FileNotFoundError('Weighted channel table %s does not exist in base_dir %s' %
-                                (weighted_cell_channel_name, base_dir))
-
-    if not os.path.exists(som_cluster_channel_avgs_path):
-        raise FileNotFoundError(
-            'Average weighted chan per cell SOM cluster file %s does not exist in base_dir %s' %
-            (cell_som_cluster_channel_avg_name, base_dir)
-        )
-
-    if not os.path.exists(meta_cluster_channel_avgs_path):
-        raise FileNotFoundError(
-            'Average weighted chan per cell meta cluster file %s does not exist in base_dir %s' %
-            (cell_meta_cluster_channel_avg_name, base_dir)
-        )
+    io_utils.validate_paths([cell_consensus_path, cell_remapped_path,
+                             som_cluster_counts_avgs_path, meta_cluster_counts_avgs_path,
+                             weighted_channel_path, som_cluster_channel_avgs_path,
+                             meta_cluster_channel_avgs_path])
 
     # verify the pixel_cluster_col provided is valid
     misc_utils.verify_in_list(
@@ -1061,9 +993,7 @@ def generate_weighted_channel_avg_heatmap(cell_cluster_channel_avg_path, cell_cl
     """
 
     # file path validation
-    if not os.path.exists(cell_cluster_channel_avg_path):
-        raise FileNotFoundError('Channel average path %s does not exist' %
-                                cell_cluster_channel_avg_path)
+    io_utils.validate_paths(cell_cluster_channel_avg_path)
 
     # verify the cell_cluster_col provided is valid
     misc_utils.verify_in_list(
@@ -1138,13 +1068,7 @@ def add_consensus_labels_cell_table(base_dir, cell_table_path, cell_data_name):
     cell_data_path = os.path.join(base_dir, cell_data_name)
 
     # file path validation
-    if not os.path.exists(cell_table_path):
-        raise FileNotFoundError('Cell table file %s does not exist' %
-                                cell_table_path)
-
-    if not os.path.exists(cell_data_path):
-        raise FileNotFoundError('Cell data file %s does not exist in base_dir %s' %
-                                (cell_data_name, base_dir))
+    io_utils.validate_paths([cell_data_path, cell_data_path])
 
     # read in the data, ensure sorted by FOV column just in case
     cell_table = pd.read_csv(cell_table_path)

ark/phenotyping/pixel_cluster_utils.py

@@ -256,8 +256,7 @@ def filter_with_nuclear_mask(fovs, tiff_dir, seg_dir, channel,
         return
 
     # raise an error if the provided seg_dir does not exist
-    if not os.path.exists(seg_dir):
-        raise FileNotFoundError('seg_dir %s does not exist' % seg_dir)
+    io_utils.validate_paths(seg_dir)
 
     # convert to path-compatible format
     if img_sub_folder is None:
@@ -603,17 +602,8 @@ def create_pixel_matrix(fovs, channels, base_dir, tiff_dir, seg_dir,
     if subset_proportion <= 0 or subset_proportion > 1:
         raise ValueError('Invalid subset percentage entered: must be in (0, 1]')
 
-    # if the base directory doesn't exist
-    if not os.path.exists(base_dir):
-        raise FileNotFoundError("base_dir %s does not exist" % base_dir)
-
-    # if the tiff dir doesn't exist
-    if not os.path.exists(tiff_dir):
-        raise FileNotFoundError("tiff_dir %s does not exist" % tiff_dir)
-
-    # if the pixel output dir doesn't exist
-    if not os.path.exists(os.path.join(base_dir, pixel_output_dir)):
-        raise FileNotFoundError("pixel_output_dir %s does not exist" % pixel_output_dir)
+    # path validation
+    io_utils.validate_paths([base_dir, tiff_dir, os.path.join(base_dir, pixel_output_dir)])
 
     # create data_dir if it doesn't already exist
     if not os.path.exists(os.path.join(base_dir, data_dir)):
@@ -794,9 +784,7 @@ def find_fovs_missing_col(base_dir, data_dir, missing_col):
     temp_path = os.path.join(base_dir, data_dir + '_temp')
 
     # verify the data path exists
-    if not os.path.exists(data_path):
-        raise FileNotFoundError('Data directory %s does not exist in base_dir %s' %
-                                (data_dir, base_dir))
+    io_utils.validate_paths(data_path)
 
     # if the temp path does not exist, either all the FOVs need to be run or none of them do
     if not os.path.exists(temp_path):
@@ -883,9 +871,7 @@ def train_pixel_som(fovs, channels, base_dir,
         return
 
     # if path to the subsetted file does not exist
-    if not os.path.exists(subsetted_path):
-        raise FileNotFoundError('Pixel subsetted directory %s does not exist in base_dir %s' %
-                                (subset_dir, base_dir))
+    io_utils.validate_paths(subsetted_path)
 
     # verify that all provided fovs exist in the folder
     files = io_utils.list_files(subsetted_path, substrs='.feather')
@@ -959,20 +945,8 @@ def cluster_pixels(fovs, channels, base_dir, data_dir='pixel_mat_data',
     norm_vals_path = os.path.join(base_dir, norm_vals_name)
     weights_path = os.path.join(base_dir, weights_name)
 
-    # if path to the preprocessed directory does not exist
-    if not os.path.exists(data_path):
-        raise FileNotFoundError('Pixel data directory %s does not exist in base_dir %s' %
-                                (data_dir, base_dir))
-
-    # if path to the normalized values file does not exist
-    if not os.path.exists(norm_vals_path):
-        raise FileNotFoundError('Normalized values file %s does not exist in base_dir %s' %
-                                (norm_vals_path, base_dir))
-
-    # if path to the weights file does not exist
-    if not os.path.exists(weights_path):
-        raise FileNotFoundError('Weights file %s does not exist in base_dir %s' %
-                                (weights_name, base_dir))
+    # path validation
+    io_utils.validate_paths([data_path, norm_vals_path, weights_path])
 
     # verify that all provided fovs exist in the folder
     # NOTE: remove the channel and pixel normalization files as those are not pixel data
@@ -1126,19 +1100,8 @@ def pixel_consensus_cluster(fovs, channels, base_dir, max_k=20, cap=3,
     som_cluster_avg_path = os.path.join(base_dir, pc_chan_avg_som_cluster_name)
     clust_to_meta_path = os.path.join(base_dir, clust_to_meta_name)
 
-    # if the path to the SOM clustered data doesn't exist
-    if not os.path.exists(data_path):
-        raise FileNotFoundError(
-            'Data dir %s does not exist in base_dir %s' %
-            (data_dir, base_dir)
-        )
-
-    # if the path to the average channel expression per SOM cluster doesn't exist
-    if not os.path.exists(som_cluster_avg_path):
-        raise FileNotFoundError(
-            'Channel avg per SOM cluster file %s does not exist in base_dir %s' %
-            (pc_chan_avg_som_cluster_name, base_dir)
-        )
+    # path validation
+    io_utils.validate_paths([data_path, som_cluster_avg_path])
 
     # if the path mapping SOM to meta clusters exists, don't re-run consensus clustering
     if os.path.exists(clust_to_meta_path):
@@ -1318,23 +1281,8 @@ def apply_pixel_meta_cluster_remapping(fovs, channels, base_dir,
     meta_cluster_avg_path = os.path.join(base_dir, pc_chan_avg_meta_cluster_name)
 
     # file path validation
-    if not os.path.exists(pixel_data_path):
-        raise FileNotFoundError('Pixel data dir %s does not exist in base_dir %s' %
-                                (pixel_data_dir, base_dir))
-
-    if not os.path.exists(pixel_remapped_path):
-        raise FileNotFoundError('Pixel remapping file %s does not exist in base_dir %s' %
-                                (pixel_remapped_name, base_dir))
-
-    if not os.path.exists(som_cluster_avg_path):
-        raise FileNotFoundError(
-            'Channel average per SOM cluster file %s does not exist in base_dir %s' %
-            (pc_chan_avg_meta_cluster_name, base_dir))
-
-    if not os.path.exists(meta_cluster_avg_path):
-        raise FileNotFoundError(
-            'Channel average per meta cluster file %s does not exist in base_dir %s' %
-            (pc_chan_avg_meta_cluster_name, base_dir))
+    io_utils.validate_paths([pixel_data_path, pixel_remapped_path, som_cluster_avg_path,
+                             meta_cluster_avg_path])
 
     # read in the remapping
     pixel_remapped_data = pd.read_csv(pixel_remapped_path)

ark/segmentation/fiber_segmentation_test.py

@@ -18,7 +18,7 @@ def test_plot_fiber_segmentation_steps():
             shutil.rmtree(os.path.join(temp_dir, 'image_data', fov))
 
         # bad directory should raise an errors
-        with pytest.raises(ValueError):
+        with pytest.raises(FileNotFoundError):
             _, _ = fiber_segmentation.plot_fiber_segmentation_steps('bad_dir', 'fov1', 'Collagen1')
 
         # bad channel should raise an errors
@@ -46,10 +46,10 @@ def test_run_fiber_segmentation():
         os.makedirs(out_dir)
 
         # bad directories should raise an error
-        with pytest.raises(ValueError):
+        with pytest.raises(FileNotFoundError):
             _ = fiber_segmentation.run_fiber_segmentation('bad_path', 'Collagen1', out_dir)
 
-        with pytest.raises(ValueError):
+        with pytest.raises(FileNotFoundError):
             _ = fiber_segmentation.run_fiber_segmentation(img_dir, 'Collagen1', 'bad_path')
 
         # bad subdirectory should raise an errors

ark/utils/data_utils.py

@@ -40,8 +40,7 @@ def save_fov_mask(fov, data_dir, mask_data, sub_dir=None, name_suffix=''):
     """
 
     # data_dir validation
-    if not os.path.exists(data_dir):
-        raise FileNotFoundError("data_dir %s does not exist" % data_dir)
+    io_utils.validate_paths(data_dir)
 
     # ensure None is handled correctly in file path generation
     if sub_dir is None:
@@ -161,12 +160,8 @@ def generate_cell_cluster_mask(fov, base_dir, seg_dir, cell_data_name,
     """
 
     # path checking
-    if not os.path.exists(seg_dir):
-        raise FileNotFoundError("seg_dir %s does not exist" % seg_dir)
-
-    if not os.path.exists(os.path.join(base_dir, cell_data_name)):
-        raise FileNotFoundError(
-            "Cell data file %s does not exist in base_dir %s" % (cell_data_name, base_dir))
+    cell_data_path = os.path.join(os.path.join(base_dir, cell_data_name))
+    io_utils.validate_paths([seg_dir, cell_data_path])
 
     # verify the cluster_col provided is valid
     verify_in_list(
@@ -277,17 +272,8 @@ def generate_pixel_cluster_mask(fov, base_dir, tiff_dir, chan_file_path,
     """
 
     # path checking
-    if not os.path.exists(tiff_dir):
-        raise FileNotFoundError("tiff_dir %s does not exist")
-
-    if not os.path.exists(os.path.join(tiff_dir, chan_file_path)):
-        raise FileNotFoundError("chan_file_path %s does not exist in tiff_dir %s"
-                                % (chan_file_path, tiff_dir))
-
-    if not os.path.exists(os.path.join(base_dir, pixel_data_dir)):
-        raise FileNotFoundError(
-            "Pixel data dir %s does not exist in base_dir %s" % (pixel_data_dir, base_dir)
-        )
+    io_utils.validate_paths([tiff_dir, os.path.join(tiff_dir, chan_file_path),
+                             os.path.join(base_dir, pixel_data_dir)])
 
     # verify the pixel_cluster_col provided is valid
     verify_in_list(

ark/utils/data_utils_test.py

@@ -686,7 +686,7 @@ def test_stitch_images_by_shape(segmentation, clustering, subdir, fovs):
             os.makedirs(data_dir)
 
             # invalid directory is provided
-            with pytest.raises(ValueError):
+            with pytest.raises(FileNotFoundError):
                 data_utils.stitch_images_by_shape('not_a_dir', stitched_dir)
 
             # no fov dirs should raise an error

ark/utils/io_utils.py

@@ -24,18 +24,18 @@ def validate_paths(paths, data_prefix=False):
     for path in paths:
         # check data prefix
         if data_prefix and not str(path).startswith('../data'):
-            raise ValueError(
+            raise FileNotFoundError(
                 f'The path, {path}, is not prefixed with \'../data\'.\n'
                 f'Be sure to add all images/files/data to the \'data\' folder, '
                 f'and to reference as \'../data/path_to_data/myfile.tif\'')
 
         if not os.path.exists(path):
             for parent in reversed(pathlib.Path(path).parents):
                 if not os.path.exists(parent):
-                    raise ValueError(
+                    raise FileNotFoundError(
                         f'A bad path, {path}, was provided.\n'
                         f'The folder, {parent.name}, could not be found...')
-            raise ValueError(
+            raise FileNotFoundError(
                 f'The file/path, {pathlib.Path(path).name}, could not be found...')