fix unit test and command line errors after renaming

CHANGELOG.md

@@ -40,7 +40,7 @@ ChangeLog history
 - added synapse annotation visualization.
 - add read-json operator
 - The code of neuroglancer operator is splitted to functions and becomes more modular. The code is more readable and maintainable.
-- add zero-filling option for read-h5 operator. If there is no such file, we fill it with zeros.
+- add zero-filling option for load-h5 operator. If there is no such file, we fill it with zeros.
 - add skip-task operator. if a result file already exists, we skip the task
 - add skip-all-zero operator. if a chunk is all zero, we skip that task.
 - add new patch inference backend: prebuilt. [PR](https://github.com/seung-lab/chunkflow/pull/250)
@@ -87,7 +87,7 @@ ChangeLog history
 - more options for generate-tasks operator
 ## Bug Fixes 
 - fix manifest by updating cloud storage to CloudFiles
-- fix read-h5 operator when only cutout size is provided
+- fix load-h5 operator when only cutout size is provided
 - fix grid size bug of generating tasks
 ## Improved Documentation 
 

README.md

@@ -48,6 +48,7 @@ After installation, You can simply type `chunkflow` and it will list all the ope
 
 | Operator Name   | Function |
 | --------------- | -------- |
+| adjust-bbox 	  | adjust the corner offset of bounding box |
 | aggregate-skeleton-fragments| Merge skeleton fragments from chunks |
 | channel-voting  | Vote across channels of semantic map |
 | cleanup         | remove empty files to clean up storage |

chunkflow/flow/flow.py

@@ -148,6 +148,21 @@ def generate_tasks(
             yield task
 
 
+@main.command('adjust-bbox')
+@click.option('--corner-offset', '-c', type=click.INT, nargs=6, default=None,
+    help='adjust bounding box corner offset')
+@operator
+def adjust_bbox(tasks, corner_offset: tuple):
+    """adjust the corner of bounding box."""
+    for task in tasks:
+        if task is not None:
+            bbox = task['bbox']
+            bbox.adjust_corner(corner_offset)
+            logging.info(f'after bounding box adjustment: {bbox.string}')
+            task['bbox'] = bbox
+        yield task
+
+
 @main.command('skip-task')
 @click.option('--prefix', '-p', required=True, type=str,
     help='the pre part of result file path')
@@ -313,7 +328,7 @@ def skip_none(tasks: dict, input_name: str, touch: bool, prefix: str, suffix: st
               help='Neuroglancer precomputed block compression algorithm.')
 @click.option('--voxel-size', '-v', type=click.INT, nargs=3, default=(40, 4, 4),
               help='voxel size or resolution of mip 0 image.')
-@click.option('--oversave-info/--no-oversave-info', default=False,
+@click.option('--overwrite-info/--no-overwrite-info', default=False,
               help='normally we should avoid overwriting info file to avoid errors.')
 @generator
 def setup_env(volume_start, volume_stop, volume_size, layer_path, 

chunkflow/flow/save_pngs.py

@@ -26,7 +26,6 @@ def __init__(self,
 
     def __call__(self, chunk: Chunk):
         assert isinstance(chunk, Chunk)
-        breakpoint()
         if not np.issubdtype(chunk.dtype, self.dtype):
             chunk = chunk.astype(self.dtype)
 

chunkflow/lib/bounding_boxes.py

@@ -287,6 +287,12 @@ def adjust(self, size: Union[Cartesian, int, tuple, list, Vec]):
         self.maxpt += size[-3:]
         return self
 
+    def adjust_corner(self, corner_offset: Union[tuple, list]):
+        if corner_offset is not None:
+            assert len(corner_offset) == 6
+            self.minpt += Cartesian.from_collection(corner_offset[:3])
+            self.maxpt += Cartesian.from_collection(corner_offset[-3:])
+
     def union(self, bbox2):
         """Merge another bounding box
 

tests/command_line.sh

@@ -7,12 +7,12 @@ chunkflow generate-tasks -c 0 0 0 -s 0 0 0 -g 1 1 1
 # echo "test nuclease..."
 # chunkflow generate-tasks --roi-start 20789 21341 17019 --chunk-size 16 128 128  plugin -f cutout_dvid_label -i bbox -o chunk
 
-chunkflow create-chunk --pattern zero skip-all-zero write-h5 -f /tmp/
+chunkflow create-chunk --pattern zero skip-all-zero save-h5 -f /tmp/
 
 echo "create a hdf5 file, then test the skip-task operator."
 # the file already exist, so we'll skip that task
 # if the skip is not successful, there is no chunk to write, we'll get an error.
-chunkflow create-chunk write-h5 -f /tmp/
+chunkflow create-chunk save-h5 -f /tmp/
 
 echo "test skip tasks..."
 chunkflow generate-tasks --roi-start 0 0 0 --chunk-size 64 64 64 skip-task --prefix /tmp/ --suffix .h5 
@@ -28,27 +28,27 @@ echo "generate summary of log..."
 chunkflow log-summary -l tests/data/log
 
 echo "test write png files..."
-chunkflow create-chunk write-pngs -o /tmp/pngs; rm -rf /tmp/pngs
+chunkflow create-chunk save-pngs -o /tmp/pngs; rm -rf /tmp/pngs
 
 echo "test normalize intensity..."
 chunkflow create-chunk normalize-intensity
 
 echo "connected component analysis..."
-chunkflow create-chunk write-h5 --file-name="/tmp/img.h5" connected-components --threshold 128 write-h5 --file-name=/tmp/seg.h5
+chunkflow create-chunk save-h5 --file-name="/tmp/img.h5" connected-components --threshold 128 save-h5 --file-name=/tmp/seg.h5
 if test -f /tmp/img.h5 ; then echo "File found"; else exit 1; fi
-chunkflow read-h5 --file-name=/tmp/img.h5
+chunkflow load-h5 --file-name=/tmp/img.h5
 
 echo "write and read nrrd file."
-chunkflow create-chunk write-nrrd -f "/tmp/img.nrrd";
-chunkflow read-nrrd -f "/tmp/img.nrrd"; 
+chunkflow create-chunk save-nrrd -f "/tmp/img.nrrd";
+chunkflow load-nrrd -f "/tmp/img.nrrd"; 
 rm /tmp/img.nrrd;
 
 echo "write and read tif file."
-chunkflow create-chunk write-tif -f "/tmp/img.tif";
-chunkflow read-tif -f "/tmp/img.tif"; 
+chunkflow create-chunk save-tif -f "/tmp/img.tif";
+chunkflow load-tif -f "/tmp/img.tif"; 
 rm /tmp/img.tif;
-chunkflow create-chunk --dtype uint16 --pattern sin write-tif -f /tmp/seg.tif
-chunkflow read-tif -f /tmp/seg.tif
+chunkflow create-chunk --dtype uint16 --pattern sin save-tif -f /tmp/seg.tif
+chunkflow load-tif -f /tmp/seg.tif
 rm /tmp/seg.tif
 
 echo "create the info file of Neuroglancer Precomputed format."
@@ -61,16 +61,18 @@ echo "write image to precomputed volume."
 # somehow, we have to separate creation of info and writing out precomputed operation!
 chunkflow \
     create-chunk --size 128 128 128 --dtype uint32 --pattern sin \
-    write-precomputed --volume-path file:///tmp/seg \
+    save-precomputed --volume-path file:///tmp/seg \
     mesh --voxel-size 8 8 8 --output-format precomputed --output-path file:///tmp/seg 
 rm -rf /tmp/seg
 
 echo "dry run of setup-environment in the cloud."
-chunkflow --dry-run --log-level info\
+chunkflow --dry-run --log-level info \
     setup-env -l "gs://my/path" --volume-start 2002 25616 12304 \
-    --volume-stop 2068 26128 12816 --max-ram-size 14 --input-patch-size 20 128 128 \
-    --output-patch-size 16 96 96 --output-patch-overlap 6 32 32 --channel-num 3 \
-    --dtype float32 -m 0 --encoding raw --voxel-size 45 16 16 --max-mip 5
+        --volume-stop 2068 26128 12816 --max-ram-size 14 \
+        --input-patch-size 20 128 128 \
+        --output-patch-size 16 96 96 --output-patch-overlap 6 32 32 \
+        --channel-num 3 --dtype float32 -m 0 --encoding raw \
+        --voxel-size 45 16 16 --max-mip 5
 
 echo "convolutional net inference."
 chunkflow --log-level debug \