TypeError when writing zarr file

[Magic-Ludo]

Hi,
I use the following code to create precomputed files from a list of .tif images:

import os
import numpy as np
import tifffile
import imageio.v3 as iio
from PIL import Image
Image.MAX_IMAGE_PIXELS = None
from cloudvolume import CloudVolume
from cloudvolume.lib import mkdir, touch

input_dir = "data_in"
output_dir = "file:///data_out/"

#encoding = "blosc"
chunk = [64, 64, 1]
base_resolution = [1800, 1800, 4000]  # X,Y,Z values in nanometers

mkdir(output_dir.replace("file://", ""))

image_files = sorted(
    [
        os.path.join(input_dir, f)
        for f in os.listdir(input_dir)
        if f.endswith(".tif")
    ]
)

first_image = iio.imread(image_files[0])
img_shape = first_image.shape
volume_size = [img_shape[0], img_shape[1], len(image_files)]

scales = [
    {
        "chunk_sizes": [chunk],
        # "encoding": encoding,
        "key": "1800_1800_4000",
        "resolution": base_resolution,
        "size": volume_size,
        "voxel_offset": [0, 0, 0],
    },
]

info = {
    "num_channels": 1,
    "layer_type": "image",
    "data_type": "uint8",
    "scales": scales,
    "type": "image",
}

vol = CloudVolume(
    "zarr://" + output_dir,
    info=info,
    mip=0,
    fill_missing=True,
    cache=False,
    parallel=False
)
vol.provenance.description = "tdTomatoPrecomputed"
vol.provenance.owners = ["[email protected]"]

vol.commit_info()
vol.commit_provenance()

progress_dir = mkdir(
    output_dir.replace("file://", "") + "progress/"
)

to_upload = list(range(0, len(image_files)))

for z, file_name in enumerate(image_files):
    print("\n Processing ", file_name, " z: ", z)
    image = tifffile.imread(file_name).astype(np.uint8)
    print(image.shape)
    image = image[..., np.newaxis]
    vol[:, :, z] = image
    touch(os.path.join(progress_dir, str(z)))

vol.commit_info()

I recently wanted to test the new feature that allows us to write zarr files (I've replaced precomputed:// by zarr:// in the above code), which avoids generating a huge number of files. However, I'm encountering this error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[34], [line 9](vscode-notebook-cell:?execution_count=34&line=9)
      [7](vscode-notebook-cell:?execution_count=34&line=7)     # image = iio.imread(file_name).astype(np.uint[8](vscode-notebook-cell:?execution_count=34&line=8))
      8     image = image[..., np.newaxis]
----> [9](vscode-notebook-cell:?execution_count=34&line=9)     vol[:, :, z] = image
     [10](vscode-notebook-cell:?execution_count=34&line=10)     touch(os.path.join(progress_dir, str(z)))
     [12](vscode-notebook-cell:?execution_count=34&line=12) # def process(z):
     [13](vscode-notebook-cell:?execution_count=34&line=13) #     print("\n Processing ", image_files[z], " z: ", z)
     [14](vscode-notebook-cell:?execution_count=34&line=14) #     image = iio.imread(image_files[z]).astype(np.uint8)
   (...)
     [24](vscode-notebook-cell:?execution_count=34&line=24) # with ProcessPoolExecutor(max_workers=8) as executor:
     [25](vscode-notebook-cell:?execution_count=34&line=25) #     executor.map(process, to_upload)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1013, in CloudVolumePrecomputed.__setitem__(self, slices, img)
   [1010](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1010) if bbox.subvoxel():
   [1011](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1011)   return
-> [1013](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1013) self.image.upload(img, bbox.minpt, self.mip, parallel=self.parallel)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:53, in readonlyguard.<locals>.guardfn(self, *args, **kwargs)
     [51](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:51) if self.readonly:
     [52](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:52)   raise exceptions.ReadOnlyException(self.meta.cloudpath)
---> [53](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:53) return fn(self, *args, **kwargs)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:194, in ZarrImageSource.upload(self, image, offset, mip, parallel, t)
    [191](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:191)     for c in range(self.meta.num_channels):
    [192](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:192)       yield image[ ispt.x:iept.x, ispt.y:iept.y, ispt.z:iept.z, c ]
--> [194](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:194) for filename, imgchunk in zip(all_chunknames, all_chunks_by_channel(all_chunks)):
    [195](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:195)   zarr_imgchunk = np.transpose(imgchunk[..., np.newaxis], axes=axis_mapping)
    [196](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:196)   binary = zarr_imgchunk.tobytes(order)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:229, in ZarrImageSource._chunknames.<locals>.ZarrChunkNamesIterator.__iter__(self)
    [227](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:227) for x,y,z in xyzrange(bbox_grid.minpt, bbox_grid.maxpt):
    [228](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:228)   for c in range(num_channels):
--> [229](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:229)     filename = sep.join([
    [230](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:230)       tchunk, str(c), str(z), str(y), str(x)
    [231](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:231)     ])
    [232](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:232)     yield cf.join(str(mip), filename)

TypeError: sequence item 0: expected str instance, int found

I tried to change line 230 in the cloudvolume/datasource/zarr/image.py file:

        for x,y,z in xyzrange(bbox_grid.minpt, bbox_grid.maxpt):
          for c in range(num_channels):
            filename = sep.join([
              HERE -> str(tchunk), str(c), str(z), str(y), str(x)
            ])
            yield cf.join(str(mip), filename)

But now another error occurs:

---------------------------------------------------------------------------
IndexError                                Traceback (most recent call last)
Cell In[4], [line 9](vscode-notebook-cell:?execution_count=4&line=9)
      [7](vscode-notebook-cell:?execution_count=4&line=7)     # image = iio.imread(file_name).astype(np.uint[8](vscode-notebook-cell:?execution_count=4&line=8))
      8     image = image[..., np.newaxis]
----> [9](vscode-notebook-cell:?execution_count=4&line=9)     vol[:, :, z] = image
     [10](vscode-notebook-cell:?execution_count=4&line=10)     touch(os.path.join(progress_dir, str(z)))
     [12](vscode-notebook-cell:?execution_count=4&line=12) # def process(z):
     [13](vscode-notebook-cell:?execution_count=4&line=13) #     print("\n Processing ", image_files[z], " z: ", z)
     [14](vscode-notebook-cell:?execution_count=4&line=14) #     image = iio.imread(image_files[z]).astype(np.uint8)
   (...)
     [24](vscode-notebook-cell:?execution_count=4&line=24) # with ProcessPoolExecutor(max_workers=8) as executor:
     [25](vscode-notebook-cell:?execution_count=4&line=25) #     executor.map(process, to_upload)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1013, in CloudVolumePrecomputed.__setitem__(self, slices, img)
   [1010](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1010) if bbox.subvoxel():
   [1011](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1011)   return
-> [1013](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/frontends/precomputed.py:1013) self.image.upload(img, bbox.minpt, self.mip, parallel=self.parallel)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:53, in readonlyguard.<locals>.guardfn(self, *args, **kwargs)
     [51](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:51) if self.readonly:
     [52](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:52)   raise exceptions.ReadOnlyException(self.meta.cloudpath)
---> [53](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/__init__.py:53) return fn(self, *args, **kwargs)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:194, in ZarrImageSource.upload(self, image, offset, mip, parallel, t)
    [191](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:191)     for c in range(self.meta.num_channels):
    [192](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:192)       yield image[ ispt.x:iept.x, ispt.y:iept.y, ispt.z:iept.z, c ]
--> [194](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:194) for filename, imgchunk in zip(all_chunknames, all_chunks_by_channel(all_chunks)):
    [195](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:195)   zarr_imgchunk = np.transpose(imgchunk[..., np.newaxis], axes=axis_mapping)
    [196](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:196)   binary = zarr_imgchunk.tobytes(order)

File ~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:192, in ZarrImageSource.upload.<locals>.all_chunks_by_channel(all_chunks)
    [190](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:190) for ispt, iept, vol_spt, vol_ept in all_chunks:
    [191](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:191)   for c in range(self.meta.num_channels):
--> [192](https://file+.vscode-resource.vscode-cdn.net/run/user/1000/gvfs/smb-share%3Aserver%3Dgrid-hs%2Cshare%3Dhou_home/corcos/CODE/facial-muscle-segmentation/Notebooks/~/.conda/envs/neurocvt/lib/python3.10/site-packages/cloudvolume/datasource/zarr/image.py:192)     yield image[ ispt.x:iept.x, ispt.y:iept.y, ispt.z:iept.z, c ]

IndexError: too many indices for array: array is 3-dimensional, but 4 were indexed

I don't know if it's the way I inject my data into the volume, but since this feature is new, I have the impression that the problem goes deeper than that.

Thanks for your help!

[william-silversmith]

Hi!

Thank you for pointing out the issues. I pushed a fix to master for the first bug. I'll look into the second but here are some things to consider:

1. zarr does not generate fewer files than precomputed unless we are talking about > 4D files. Precomputed has a sharded format that will generate many fewer files than zarr. see: https:/seung-lab/cloud-volume/wiki/Creating-a-Sharded-Image-from-Scratch (note: these operations can be performed without Igneous now, I should update the wiki article).
2. The implementation of zarr in CV is custom and was written specifically for 5D timeseries, color 3D spatial volumes. I should probably update it to be a bit more general.
3. You could consider using a larger chunk size to reduce the number of files.

[Magic-Ludo]

I agree, thank you for your reply.
In fact, the data I'm handling is just in 3D color.

I use a chunk size of 64 because when I go to 128, the loading time is much longer.

I'll stick with the precomputed format then, thanks!