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losonczylab / sima

Python package for analysis of dynamic fluorescence microscopy data
GNU General Public License v2.0
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Python 3.7 issue creating Tiff sequences and ROI object #254

Open Saksham20 opened 4 years ago

Saksham20 commented 4 years ago

Similar to #253, With the example dataset for TIFF in the repo, when I create a sequence object like: 

sequences_tiff = [sima.Sequence.join(sima.Sequence.create('TIFF', base_dir + 'example_Ch1.tif'),sima.Sequence.create('TIFF', base_dir + 'example_Ch2.tif'))]

I get an error(works in python <3.7): 

[Command: python -u '$\py2_sima.py']
Traceback (most recent call last):
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 631, in __iter__
    for _ in range(self._num_planes)], 0)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 631, in <listcomp>
    for _ in range(self._num_planes)], 0)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 629, in <listcomp>
    for _ in range(self._num_channels)],
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "$\py2_sima.py", line 34, in <module>
    sequences_tiff = [sima.Sequence.join(sima.Sequence.create('TIFF', base_dir + 'example_Ch1.tif'),sima.Sequence.create('TIFF', base_dir + 'example_Ch2.tif'))]
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 276, in join
    return _Joined_Sequence(sequences)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 966, in __init__
    shape = seq.shape[:-1]
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 199, in shape
    return (len(self),) + self._get_frame(0).shape
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 680, in __len__
    self._len = sum(1 for _ in self)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 680, in <genexpr>
    self._len = sum(1 for _ in self)
RuntimeError: generator raised StopIteration
[Finished in 3.795s]

I am however able to create sequence objects for numpy and hdf5:

cycle1_channel1 = np.random.rand(100, 1, 128, 128, 1)
cycle1_channel2 = np.random.rand(100, 1, 128, 128, 1)
cycle2_channel1 = np.random.rand(100, 1, 128, 128, 1)
cycle2_channel2 = np.random.rand(100, 1, 128, 128, 1)
sequences_np = [sima.Sequence.join(
                  sima.Sequence.create('ndarray', cycle1_channel1),
                  sima.Sequence.create('ndarray', cycle1_channel2)),
                  sima.Sequence.join(
                  sima.Sequence.create('ndarray', cycle2_channel1),
                  sima.Sequence.create('ndarray', cycle2_channel2))]`
sequences_hdf5 = [sima.Sequence.create('HDF5', base_dir + 'example.h5', 'yxt')]

But, with np object when I create a ROI object it thrown an error: 

segmentation_approach = sima.segment.PlaneCA1PC(
    channel='Green',
    num_pcs=30,
    max_dist=(3, 6),
    spatial_decay=(3, 6),
    cut_max_pen=0.10,
    cut_min_size=50,
    cut_max_size=150,
    x_diameter=14,
    y_diameter=7,
    circularity_threhold=.5,
    min_roi_size=20,
    min_cut_size=40
)

rois = dataset_corr_np.segment(segmentation_approach, label='auto_ROIs')

ERROR:

[Command: python -u '$\py3_sima.py']
Estimating model parameters.
Estimating displacements for cycle  0
Estimating displacements for cycle  1
Traceback (most recent call last):
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\oPCA.py", line 249, in __iter__
    raise StopIteration
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "$\py3_sima.py", line 95, in <module>
    rois = dataset_corr_np.segment(segmentation_approach, label='auto_ROIs')
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\imaging.py", line 913, in segment
    rois = strategy.segment(self)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\segment.py", line 46, in segment
    rois = self._segment(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\segment.py", line 88, in checked_func
    return func(self, dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\ca1pc.py", line 276, in _segment
    return self._normcut_method.segment(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\segment.py", line 46, in segment
    rois = self._segment(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\segment.py", line 88, in checked_func
    return func(self, dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\normcut.py", line 500, in _segment
    affinity = params['affinity_method'].calculate(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\normcut.py", line 406, in calculate
    self._setup(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\ca1pc.py", line 162, in _setup
    super(AffinityMatrixCA1PC, self)._setup(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\normcut.py", line 403, in _setup
    self._correlations = self._calculate_correlations(dataset)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\normcut.py", line 393, in _calculate_correlations
    num_pcs=self._params['num_pcs'], verbose=self._params['verbose'])
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\normcut.py", line 307, in _offset_corrs
    verbose=verbose)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\oPCA.py", line 301, in dataset_opca
    DatasetIterable(dataset, ch), num_pcs=num_pcs, verbose=verbose)
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\segment\oPCA.py", line 109, in EM_oPCA
    _opca._Z_update(Z, U, data)
  File "sima\segment\_opca.pyx", line 84, in sima.segment._opca._Z_update
RuntimeError: generator raised StopIteration
Exception ignored in: <function _Sequence_HDF5.__del__ at 0x00000000107FB798>
Traceback (most recent call last):
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\sima\sequence.py", line 817, in __del__
  File "$\AppData\Local\Programs\Python\Python37\lib\site-packages\h5py\_hl\files.py", line 431, in close
  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py\h5f.pyx", line 267, in h5py.h5f.get_obj_ids
  File "h5py\h5i.pyx", line 40, in h5py.h5i.wrap_identifier
ImportError: sys.meta_path is None, Python is likely shutting down
[Finished in 26.508s]