implement test up to luigi task

mobie · Feb 9, 2024 · abba28e · abba28e
1 parent 9b22618
commit abba28e
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Showing 3 changed files with 26 additions and 4 deletions.
diff --git a/mobie/import_data/image.py b/mobie/import_data/image.py
@@ -43,7 +43,9 @@ def import_image_data(in_path, in_key, out_path,
             raise NotImplementedError("Selection of sub-arrays only possible with OME-Zarr output.")
 
     if selected_input_channel:
-        if len(selected_input_channel) < 2:
+        if type(selected_input_channel) is int:
+            selected_input_channel = [0, selected_input_channel]
+        elif len(selected_input_channel) < 2:
             # if only one element, we assume relevant image stack dimension is 0 (like channel for multi-channel tifs).
             selected_input_channel = [0, selected_input_channel[0]]
         elif len(selected_input_channel) > 2:
@@ -52,7 +54,7 @@ def import_image_data(in_path, in_key, out_path,
         with open_file(in_path, mode="r") as f:
             shape = f[in_key].shape
             newshape = list(shape)
-            _unused_ = newshape.pop(selected_input_channel[1])
+            _unused_ = newshape.pop(selected_input_channel[0])
 
         roi_begin = [0] * len(shape)
         roi_end = list(shape)

diff --git a/mobie/import_data/utils.py b/mobie/import_data/utils.py
@@ -1,5 +1,6 @@
 import json
 import os
+import numpy as np
 
 import luigi
 import nifty.distributed as ndist
@@ -47,12 +48,17 @@ def compute_node_labels(seg_path, seg_key,
     return data
 
 
-def check_input_data(in_path, in_key, resolution, require3d, channel):
+def check_input_data(in_path, in_key, resolution, require3d, channel, roi_begin=None, roi_end=None):
     # TODO to support data with channel, we need to support downscaling with channels
     if channel is not None:
         raise NotImplementedError
     with open_file(in_path, "r") as f:
         ndim = f[in_key].ndim
+        if any((roi_begin, roi_end)):
+            # reduce singleton dimensons
+            if any(np.array(roi_end) - np.array(roi_begin) == 1):
+                ndim = ndim - np.sum(np.array(roi_end) - np.array(roi_begin) == 1)
+
     if require3d and ndim != 3:
         raise ValueError(f"Expect 3d data, got ndim={ndim}")
     if len(resolution) != ndim:
@@ -73,7 +79,7 @@ def downscale(in_path, in_key, out_path,
     config_dir = os.path.join(tmp_folder, "configs")
     # ome.zarr can also be written in 2d, all other formats require 3d
     require3d = metadata_format != "ome.zarr"
-    check_input_data(in_path, in_key, resolution, require3d, channel)
+    check_input_data(in_path, in_key, resolution, require3d, channel, roi_begin=roi_begin, roi_end=roi_end)
     write_global_config(config_dir, block_shape=block_shape, require3d=require3d,
                         roi_begin=roi_begin, roi_end=roi_end)
 

diff --git a/test/test_image_data.py b/test/test_image_data.py
@@ -314,6 +314,20 @@ def test_skip_metadata(self):
         self.check_data(os.path.join(self.root, self.dataset_name), im_name)
 
 
+    def test_input_channel(self):
+        path1 = os.path.join(self.test_folder, '3ch.h5')
+        key = 'data'
+        self.make_hdf5_data(path1, key, shape=(3,128,128))
+
+        mobie.add_image(path1, key, self.root, self.dataset_name, '3ch_test',
+                        resolution=(1, 1), scale_factors=[[2,2]],
+                        chunks=(64, 64), tmp_folder=self.tmp_folder,
+                        file_format='ome.zarr',
+                        target="local", max_jobs=self.max_jobs, selected_input_channel=1)
+
+
+        pass
+
     #
     # data validation
     #