trackpy.batch only works with processes = 1

[ggomes-altos]

Python 3.12.4 trackpy 0.6.4

The following runs without error: f = tp.batch(frames, 11, invert=False, minmass=500, processes=1)

whereas processes = 2 gives a long error message ultimately ending in TiffFileError: corrupted tag list at offset 254920375

and processes = 'auto' gives a warning ( ValueError: need at most 63 handles, got a sequence of length 66 ) which disappears and is replaced with the Frame number 1 and number of features, but the computation never ends.

Happy to include full error messages if necessary.

[nkeim]

Thanks for this report. Do you know what version of pims you have, and which package is installed for reading tiffs? (usually libtiff or tifffile)

On Aug 8, 2024, at 7:01 PM, ggomes-altos @.***> wrote:

Python 3.12.4 trackpy 0.6.4

The following runs without error: f = tp.batch(frames, 11, invert=False, minmass=500, processes=1)

whereas processes = 2 gives a long error message ultimately ending in TiffFileError: corrupted tag list at offset 254920375

and processes = 'auto' gives a warning ( ValueError: need at most 63 handles, got a sequence of length 66 ) which disappears and is replaced with the Frame number 1 and number of features, but the computation never ends.

Happy to include full error messages if necessary.

— Reply to this email directly, view it on GitHubhttps://github.com/soft-matter/trackpy/issues/771, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAWY23NWV4XON3CF3IULEZTZQP2DRAVCNFSM6AAAAABMHMNIRKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ2TMNZYGE4DIOA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[ggomes-altos]

Hi sorry for the delayed response.

I have pims 0.7 libtiff 4.6.0 tifffile 2023.4.12

I think tiffffile is doing the tiff reading since in the lowest level of the error message it seems to be using the tifffile package:

---

ValueError Traceback (most recent call last) ~\AppData\Local\Temp\ipykernel_18640\387384096.py in ?() ----> 1 f = tp.batch(frames, 11, invert=False, minmass=500, processes=2);

A_path\Lib\site-packages\trackpy\feature.py in ?(frames, diameter, output, meta, processes, after_locate, **kwargs) 577 output.put(features) 578 finally: 579 if pool: 580 # Ensure correct termination of Pool --> 581 pool.terminate() 582 583 if output is None: 584 if len(all_features) > 0:

A_path\Lib\site-packages\slicerator__init.py in ?(self, i) 183 def getitem__(self, i): 184 """Getitem supports repeated slicing via Slicerator objects.""" 185 indices, new_length = key_to_indices(i, len(self)) 186 if new_length is None: --> 187 return self._get(indices) 188 else: 189 return cls(self, indices, new_length, propagate_attrs)

A_path\Lib\site-packages\pims\base_frames.py in ?(self, key) 97 def getitem(self, key): 98 """getitem is handled by Slicerator. In all pims readers, the data 99 returning function is get_frame.""" --> 100 return self.get_frame(key)

A_path\Lib\site-packages\pims\tiff_stack.py in ?(self, j) 129 def get_frame(self, j): 130 t = self._tiff[j] --> 131 data = t.asarray() 132 return Frame(data, frame_no=j, metadata=self._read_metadata(t))

A_path\Lib\site-packages\tifffile\tifffile.py in ?(self, out, squeeze, lock, maxworkers) 8835 f'{self!r} reading array from closed file', UserWarning 8836 ) 8837 fh.open() 8838 fh.seek(self.dataoffsets[0]) -> 8839 result = fh.read_array( 8840 keyframe.parent.byteorder + keyframe._dtype.char, 8841 product(keyframe.shaped), 8842 out=out,

A_apth\Lib\site-packages\tifffile\tifffile.py in ?(self, dtype, count, offset, out) 14214 ) 14215 n = nbytes 14216 14217 if n != nbytes:

14218 raise ValueError(f'failed to read {nbytes} bytes, got {n}') 14219 14220 if not result.dtype.isnative: 14221 if not dtype.isnative: