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python-microscopy / python-microscopy

The python-microscopy environment - an open-source package for light microscopy
http://www.python-microscopy.org
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[BUG] checksum fit regression #1202

Closed barentine closed 2 years ago

barentine commented 2 years ago

Describe the bug localizing from PYMEAcquire simulated h5 file with a cluster of one, ChecksumFR

===========================================================================
Error in rule: 000000-aaec8bbfc4e142cc8315c32e695fac12 running task: 130 on WEM24C:69744

taskDescr:
----------
{'id': '000000-aaec8bbfc4e142cc8315c32e695fac12~130', 'type': 'localization', 'taskdef': {'frameIndex': '130', 'metadata': 'PYME-CLUSTER://WEM24C/aesb/2021_8_9/analysis/9_8_series_A_checksum0.h5r.json'}, 'inputs': {'frames': 'C:\\Users\\aesb\\PYMEData\\aesb\\2021_8_9\\9_8_series_A.h5'}, 'outputs': {'fitResults': 'http://127.0.0.1:64832/__aggregate_h5r/aesb/2021_8_9/analysis/9_8_series_A_checksum0.h5r/FitResults', 'driftResults': 'http://127.0.0.1:64832/__aggregate_h5r/aesb/2021_8_9/analysis/9_8_series_A_checksum0.h5r/DriftResults'}}

Traceback:
----------
Traceback (most recent call last):
  File "c:\userfiles\andrew\code\python-microscopy\PYME\cluster\taskWorkerHTTP.py", line 309, in computeLoop
    res = task()
  File "c:\userfiles\andrew\code\python-microscopy\PYME\localization\remFitBuf.py", line 545, in __call__
    self.res[i] = fitFac.FromPoint(p.x, p.y)
  File "c:\userfiles\andrew\code\python-microscopy\PYME\localization\FitFactories\ChecksumFR.py", line 58, in FromPoint
    ch_sigma = zlib.crc32(sigma.data)
BufferError: memoryview: underlying buffer is not C-contiguous

for reference:

>>> image.dataSource.h5File.root.ImageData
/ImageData (EArray(535, 256, 256), shuffle, zlib(2)) ''
  atom := UInt16Atom(shape=(), dflt=0)
  maindim := 0
  flavor := 'numpy'
  byteorder := 'little'
  chunkshape := (2, 256, 256)

To Reproduce Steps to reproduce the behavior:

  1. PYMEAcquire
  2. simulate some points, save to h5
  3. PYMEImage open the h5
  4. PYMEClusterOfOne
  5. localize with checksumFR and Background -30:0, using 25th percentile in fit
  6. see error

Platform (please complete the following information - or copy-paste from error dialog if shown):

David-Baddeley commented 2 years ago

Suspect this is numpy version related, in any case should be fixable with a ravel() call or similar.

On Wed, 16 Feb 2022, 07:00 barentine, @.***> wrote:

Describe the bug localizing from PYMEAcquire simulated h5 file with a cluster of one, ChecksumFR

=========================================================================== Error in rule: 000000-aaec8bbfc4e142cc8315c32e695fac12 running task: 130 on WEM24C:69744

taskDescr:

{'id': '000000-aaec8bbfc4e142cc8315c32e695fac12~130', 'type': 'localization', 'taskdef': {'frameIndex': '130', 'metadata': 'PYME-CLUSTER://WEM24C/aesb/2021_8_9/analysis/9_8_series_A_checksum0.h5r.json'}, 'inputs': {'frames': 'C:\Users\aesb\PYMEData\aesb\2021_8_9\9_8_series_A.h5'}, 'outputs': {'fitResults': 'http://127.0.0.1:64832/__aggregate_h5r/aesb/2021_8_9/analysis/9_8_series_A_checksum0.h5r/FitResults', 'driftResults': 'http://127.0.0.1:64832/__aggregate_h5r/aesb/2021_8_9/analysis/9_8_series_A_checksum0.h5r/DriftResults'}}

Traceback:

Traceback (most recent call last): File "c:\userfiles\andrew\code\python-microscopy\PYME\cluster\taskWorkerHTTP.py", line 309, in computeLoop res = task() File "c:\userfiles\andrew\code\python-microscopy\PYME\localization\remFitBuf.py", line 545, in call self.res[i] = fitFac.FromPoint(p.x, p.y) File "c:\userfiles\andrew\code\python-microscopy\PYME\localization\FitFactories\ChecksumFR.py", line 58, in FromPoint ch_sigma = zlib.crc32(sigma.data) BufferError: memoryview: underlying buffer is not C-contiguous

for reference:

image.dataSource.h5File.root.ImageData /ImageData (EArray(535, 256, 256), shuffle, zlib(2)) '' atom := UInt16Atom(shape=(), dflt=0) maindim := 0 flavor := 'numpy' byteorder := 'little' chunkshape := (2, 256, 256)

To Reproduce Steps to reproduce the behavior:

  1. PYMEAcquire
  2. simulate some points, save to h5
  3. PYMEImage open the h5
  4. PYMEClusterOfOne
  5. localize with checksumFR and Background -30:0, using 25th percentile in fit
  6. see error

Platform (please complete the following information - or copy-paste from error dialog if shown):

  • OS: Win10
  • Python version: 3.7
  • numpy version: 1.19
  • wxpython version [if a UI bug]: 4.0.4

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