add channels parameter for load-h5 operator; fix the progress bar of …

…load-pngs operator

chunkflow/chunk/base.py

@@ -265,6 +265,7 @@ def from_h5(cls, file_name: str,
                 voxel_offset: tuple=None,
                 dataset_path: str = None,
                 voxel_size: tuple = None,
+                channels: str = None,
                 cutout_start: tuple = None,
                 cutout_stop: tuple = None,
                 cutout_size: tuple = None,
@@ -336,11 +337,18 @@ def from_h5(cls, file_name: str,
 
             assert len(cutout_start) == 3
             assert len(cutout_stop) == 3
-            dset = dset[...,
-                cutout_start[0]-voxel_offset[0]:cutout_stop[0]-voxel_offset[0],
-                cutout_start[1]-voxel_offset[1]:cutout_stop[1]-voxel_offset[1],
-                cutout_start[2]-voxel_offset[2]:cutout_stop[2]-voxel_offset[2],
-            ]
+            if channels is None:
+                dset = dset[...,
+                    cutout_start[0]-voxel_offset[0]:cutout_stop[0]-voxel_offset[0],
+                    cutout_start[1]-voxel_offset[1]:cutout_stop[1]-voxel_offset[1],
+                    cutout_start[2]-voxel_offset[2]:cutout_stop[2]-voxel_offset[2],
+                ]
+            else:
+                dset = dset[ eval(channels),
+                    cutout_start[0]-voxel_offset[0]:cutout_stop[0]-voxel_offset[0],
+                    cutout_start[1]-voxel_offset[1]:cutout_stop[1]-voxel_offset[1],
+                    cutout_start[2]-voxel_offset[2]:cutout_stop[2]-voxel_offset[2],
+                ]
 
 
         print(f"""read from HDF5 file: {file_name} and start with {cutout_start}, \

chunkflow/flow/flow.py

@@ -990,6 +990,8 @@ def save_tif(tasks, input_chunk_name: str, file_name: str, dtype: str, compressi
 @click.option('--voxel-size', '-x', type=click.INT, nargs=3, 
     default=None, callback=default_none, 
     help='physical size of voxels. The unit is assumed to be nm.')
+@click.option('--channels', '-c', type=str, default=None,
+    help='selected channels.')
 @click.option('--cutout-start', '-t', type=click.INT, nargs=3, callback=default_none,
               help='cutout voxel offset in the array')
 @click.option('--cutout-stop', '-p', type=click.INT, nargs=3, callback=default_none,
@@ -1006,7 +1008,7 @@ def save_tif(tasks, input_chunk_name: str, file_name: str, dtype: str, compressi
 @operator
 def load_h5(tasks, name: str, file_name: str, dataset_path: str,
             dtype: str, layer_type: str, voxel_offset: tuple, 
-            voxel_size: tuple, cutout_start: tuple, 
+            voxel_size: tuple, channels: str, cutout_start: tuple, 
             cutout_stop: tuple, cutout_size: tuple, set_bbox: bool,
             remove_empty: bool, output_chunk_name: str):
     """Read HDF5 files."""
@@ -1035,6 +1037,7 @@ def load_h5(tasks, name: str, file_name: str, dataset_path: str,
                 dataset_path=dataset_path,
                 voxel_offset=voxel_offset,
                 voxel_size=voxel_size,
+                channels = channels,
                 cutout_start=cutout_start_tmp,
                 cutout_size=cutout_size_tmp,
                 cutout_stop=cutout_stop_tmp,
@@ -1048,8 +1051,6 @@ def load_h5(tasks, name: str, file_name: str, dataset_path: str,
                 print(f'remove {file_name}')
                 os.remove(file_name)
 
-            # if len(chunk.array) == 0:
-            #     breakpoint()
             if chunk is not None and dtype is not None:
                 chunk = chunk.astype(dtype)
 

chunkflow/flow/load_pngs.py

@@ -44,7 +44,7 @@ def load_png_images(
         shape = Cartesian(len(file_names), img.shape[0], img.shape[1])
         bbox = BoundingBox.from_delta(voxel_offset, shape)
     else:
-        for z in tqdm( range(bbox.start[0], bbox.stop[0]) ):
+        for z in range(bbox.start[0], bbox.stop[0]):
             file_name = f'{path_prefix}{z:0>{digit_num}d}.png'
             file_name = os.path.expanduser(file_name)
             file_names.append(file_name)
@@ -55,7 +55,7 @@ def load_png_images(
         voxel_size=voxel_size
     )
 
-    for z_offset, file_name in enumerate(file_names):
+    for z_offset, file_name in tqdm(enumerate(file_names)):
         if os.path.exists(file_name):
             img = load_image(file_name)
             img = img.astype(dtype=dtype)