Path loader has no fallback to relative paths

[cniedwor]

See title - when a brain is copied someplace else, the path file needs to be updated by hand since the image loader does not attempt to locate the images relative to the image path file.

[crousseau]

Can you confirm this pertains to loading image sequence from text file

[cniedwor]

Yes:

cniedwo@MS-workstation:~/swc_github/amap_python$ python3 amap/main.py /media/cniedwo/Data/epo/1058_stitching_2/1058-Ch_0.txt amap-python-test /media/cniedwo/Data/epo/countTest/1058/amap -x 0.002 -y 0.002 --save-unfiltered --generate-outlines -p
Preprocessing
Loading images:   0%|                                                                                                                                                                                                    | 0/1600 [00:00<?, ?plane/s]
Traceback (most recent call last):
  File "amap/main.py", line 111, in <module>
    print("Segmentation finished. Result can be found here: {}".format(process(args)))
  File "amap/main.py", line 83, in process
    _args.x_pixel_mm, _args.y_pixel_mm, _args.z_pixel_mm)
  File "/home/cniedwo/swc_github/amap_python/amap/brain/brain_processor.py", line 38, in __init__
    self.target_brain = bio.load_any(self.target_brain_path, x_scaling, y_scaling, z_scaling)
  File "/home/cniedwo/swc_github/amap_python/amap/brain/brain_io.py", line 46, in load_any
    img = load_img_sequence(src_path, x_scaling_factor, y_scaling_factor)
  File "/home/cniedwo/swc_github/amap_python/amap/brain/brain_io.py", line 85, in load_img_sequence
    return load_from_paths_sequence(paths, x_scaling_factor, y_scaling_factor)
  File "/home/cniedwo/swc_github/amap_python/amap/brain/brain_io.py", line 90, in load_from_paths_sequence
    img = tifffile.imread(p)
  File "/usr/local/lib/python3.5/dist-packages/tifffile-0.14.0-py3.5-linux-x86_64.egg/tifffile/tifffile.py", line 424, in imread
    with TiffFile(files, **kwargs_file) as tif:
  File "/usr/local/lib/python3.5/dist-packages/tifffile-0.14.0-py3.5-linux-x86_64.egg/tifffile/tifffile.py", line 1677, in __init__
    fh = FileHandle(arg, mode='rb', name=name, offset=offset, size=size)
  File "/usr/local/lib/python3.5/dist-packages/tifffile-0.14.0-py3.5-linux-x86_64.egg/tifffile/tifffile.py", line 4548, in __init__
    self.open()
  File "/usr/local/lib/python3.5/dist-packages/tifffile-0.14.0-py3.5-linux-x86_64.egg/tifffile/tifffile.py", line 4559, in open
    self._fh = open(self._file, self._mode)
FileNotFoundError: [Errno 2] No such file or directory: '/media/cniedwo/Data/1058_stitching_2/ch00/1058_45_00000_ch00.tif'

The Error disappears as soon as the paths in the text file are corrected.