removed unneeded function

caliban_toolbox/pipeline.py

@@ -55,8 +55,8 @@ def save_stitched_npzs(stitched_channels, stitched_labels, save_dir):
     """Takes corrected labels and channels and saves them into NPZ format
 
     Args:
-        stitched_channels: original channel data
-        stitched_labels: stitched labels
+        stitched_channels: xarray containing original channel data
+        stitched_labels: xarray containing stitched labels
     """
 
     for i in range(stitched_channels.shape[0]):
@@ -67,23 +67,6 @@ def save_stitched_npzs(stitched_channels, stitched_labels, save_dir):
         np.savez(save_path, X=X, y=y)
 
 
-def process_stitched_data(base_dir):
-    """Takes stitched output and creates folder of NPZs for review
-
-    Args:
-        base_dir: directory to read from
-    """
-
-    stitched_labels = xr.load_dataarray(os.path.join(base_dir, 'output', 'stitched_labels.xr'))
-    channel_data = xr.load_dataarray(os.path.join(base_dir, 'channel_data.xr'))
-
-    stitched_folder = os.path.join(base_dir, 'stitched_npzs')
-    os.makedirs(stitched_folder)
-
-    save_stitched_npzs(stitched_channels=channel_data, stitched_labels=stitched_labels,
-                       save_dir=stitched_folder)
-
-
 def concatenate_npz_files(npz_list):
     """Takes a list of NPZ files and combines the X and y keys of each together
 

caliban_toolbox/pipeline_test.py

@@ -75,24 +75,6 @@ def test_save_stitched_npzs():
         assert np.all(np.isin(npzs, npz_names))
 
 
-def test_process_stitched_data():
-    channels = np.zeros((4, 100, 100, 2))
-    labels = np.zeros((4, 100, 100, 1))
-
-    coords_labels = [['fov1', 'fov2', 'fov3', 'fov4'], range(100), range(100), [0]]
-    coords_channels = [['fov1', 'fov2', 'fov3', 'fov4'], range(100), range(100), range(2)]
-    dims = ['fovs', 'rows', 'cols', 'channels']
-    labels = xr.DataArray(labels, coords=coords_labels, dims=dims)
-    channels = xr.DataArray(channels, coords=coords_channels, dims=dims)
-
-    with tempfile.TemporaryDirectory() as temp_dir:
-        os.makedirs(os.path.join(temp_dir, 'output'))
-        labels.to_netcdf(os.path.join(temp_dir, 'output', 'stitched_labels.xr'))
-        channels.to_netcdf(os.path.join(temp_dir, 'channel_data.xr'))
-
-        pipeline.process_stitched_data(temp_dir)
-
-
 def test_concatenate_npz_files():
     npz_num = 5
     npz_list = _make_npz_files(npz_num=npz_num)

caliban_toolbox/reshape_data.py

@@ -193,6 +193,9 @@ def reconstruct_image_stack(crop_dir, verbose=True):
         Args:
             crop_dir: full path to directory with cropped images
             verbose: flag to control print statements
+
+        Returns:
+            stitched_images: xarray containing the stitched image stack
         """
 
     # sanitize inputs
@@ -225,4 +228,4 @@ def reconstruct_image_stack(crop_dir, verbose=True):
     stitched_xr = xr.DataArray(data=image_stack, coords=coordinate_labels,
                                dims=dimension_labels)
 
-    stitched_xr.to_netcdf(os.path.join(crop_dir, 'stitched_images.xr'))
+    return stitched_xr

caliban_toolbox/reshape_data_test.py

@@ -178,9 +178,7 @@ def test_reconstruct_image_stack():
         io_utils.save_npzs_for_caliban(X_data=X_cropped, y_data=y_cropped, original_data=X_data,
                                        log_data=log_data, save_dir=temp_dir)
 
-        reshape_data.reconstruct_image_stack(crop_dir=temp_dir)
-
-        stitched_imgs = xr.open_dataarray(os.path.join(temp_dir, 'stitched_images.xr'))
+        stitched_imgs = reshape_data.reconstruct_image_stack(crop_dir=temp_dir)
 
         # dims are the same
         assert np.all(stitched_imgs.shape == y_data.shape)
@@ -219,8 +217,7 @@ def test_reconstruct_image_stack():
                                        blank_labels="include",
                                        save_format="npz", verbose=False)
 
-        reshape_data.reconstruct_image_stack(temp_dir)
-        stitched_imgs = xr.open_dataarray(os.path.join(temp_dir, 'stitched_images.xr'))
+        stitched_imgs = reshape_data.reconstruct_image_stack(temp_dir)
 
         assert np.all(stitched_imgs.shape == y_data.shape)
         assert np.all(np.equal(stitched_imgs[0, :, 0, 0, 0, 0, 0], tags))
@@ -272,8 +269,7 @@ def test_reconstruct_image_stack():
                                        blank_labels="include",
                                        save_format="npz", verbose=False)
 
-        reshape_data.reconstruct_image_stack(temp_dir)
-        stitched_imgs = xr.open_dataarray(os.path.join(temp_dir, 'stitched_images.xr'))
+        stitched_imgs = reshape_data.reconstruct_image_stack(temp_dir)
 
         assert np.all(stitched_imgs.shape == y_data.shape)