construct a MultiPageTIFF: Error

[ObadaM]

I am getting an error when I apply the following code:

files = glob.glob('data/*.tif')
sequences = [sima.Sequence.join(*[sima.Sequence.create('TIFF', tif_file) ]) for tif_file in files]

Error

Traceback (most recent call last):
  File "/home/l-01-314/PycharmProjects/test/Motion_Correction.py", line 32, in <module>
    sequences = [sima.Sequence.join(*[sima.Sequence.create('TIFF', folder) ]) for folder in pop]
  File "/home/l-01-314/PycharmProjects/test/Motion_Correction.py", line 32, in <listcomp>
    sequences = [sima.Sequence.join(*[sima.Sequence.create('TIFF', folder) ]) for folder in pop]
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 245, in join
    return _Joined_Sequence(sequences)
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 748, in __init__
    shape = seq.shape[:-1]
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 167, in shape
    return (len(self),) + self._get_frame(0).shape
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 558, in __len__
    self._len = sum(1 for _ in self)
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 558, in <genexpr>
    self._len = sum(1 for _ in self)
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 509, in __iter__
    for _ in range(self._num_planes)], 0)
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 509, in <listcomp>
    for _ in range(self._num_planes)], 0)
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 507, in <listcomp>
    for _ in range(self._num_channels)],
  File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 536, in _iter_pages
    images.seek(idx)
  File "/usr/anaconda3/lib/python3.5/site-packages/PIL/TiffImagePlugin.py", line 934, in seek
    self.im = Image.core.new(self.mode, self.size)
ValueError: unrecognized mode

is there any idea why I am getting this error ?

[nbdanielson]

Can you try installing version 1.3.0 to make sure this isn't an issue with
the version we just released?

On Tue, May 31, 2016 at 11:56 AM, ObadaM [email protected] wrote:

I am getting an error when I apply the following code:

files = glob.glob('data/.tif')
sequences = [sima.Sequence.join([sima.Sequence.create('TIFF', tif_file) ]) for tif_file in files]

Error

Traceback (most recent call last):
File "/home/l-01-314/PycharmProjects/test/Motion_Correction.py", line 32, in
sequences = [sima.Sequence.join([sima.Sequence.create('TIFF', folder) ]) for folder in pop]
File "/home/l-01-314/PycharmProjects/test/Motion_Correction.py", line 32, in
sequences = [sima.Sequence.join([sima.Sequence.create('TIFF', folder) ]) for folder in pop]
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 245, in join
return _Joined_Sequence(sequences)
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 748, in init
shape = seq.shape[:-1]
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 167, in shape
return (len(self),) + self._get_frame(0).shape
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 558, in len
self._len = sum(1 for _ in self)
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 558, in
self._len = sum(1 for _ in self)
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 509, in iter
for _ in range(self._num_planes)], 0)
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 509, in
for _ in range(self._num_planes)], 0)
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 507, in
for _ in range(self._num_channels)],
File "/usr/anaconda3/lib/python3.5/site-packages/sima-1.3.1-py3.5-linux-x86_64.egg/sima/sequence.py", line 536, in _iter_pages
images.seek(idx)
File "/usr/anaconda3/lib/python3.5/site-packages/PIL/TiffImagePlugin.py", line 934, in seek
self.im = Image.core.new(self.mode, self.size)
ValueError: unrecognized mode

is there any idea why I am getting this error ?

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[ObadaM]

@nbdanielson
I run this command to install the previous version:

pip install sima==1.3.0

But I could not install it, I got the following:

Building wheels for collected packages: sima
  Running setup.py bdist_wheel for sima ... error
  Complete output from command /usr/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-m3nq4i26/sima/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmp6jvwikj1pip-wheel- --python-tag cp35:
.
.
.
.
 ----------------------------------------
  Failed building wheel for sima
  Running setup.py clean for sima
Failed to build sima
Installing collected packages: sima
  Running setup.py install for sima ... error
    Complete output from command /usr/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-m3nq4i26/sima/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-qhx0bibj-record/install-record.txt --single-version-externally-managed --compile:
.
.
.
.
    ----------------------------------------
Command "/usr/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-m3nq4i26/sima/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-qhx0bibj-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-m3nq4i26/sima/

[pkaifosh]

Can you please confirm the format of your data, i.e. what is contained in each TIFF file?
Do you have PIL or pillow installed?