problem with running the microscopy pipeline

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This issue affects

- [ ] Centrality estimation (gpseqc_estimate)
What did you do (e.g., steps to reproduce)

I tried to run GPSeq microscopy pipeline.
What did you expect to happen?

To get beautiful YFISH plots as an output :)
What happened instead?

The pipeline failed by the segmentation step.
* Looking for nuclei *

 Current condition: "iTK226_070618_001"...
Traceback (most recent call last):
  File "/usr/local/bin/gpseq_anim", line 6, in <module>
    exec(compile(open(__file__).read(), __file__, 'exec'))
  File "/home/bicro/Desktop/ggcode/pygpseq/bin/gpseq_anim", line 388, in <module>
    gpi = gpi.run()
  File "/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/main.py", line 716, in run
    self.run_segmentation(**kwargs)
  File "/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/main.py", line 914, in run_segmentation
    [c.find_nuclei(**kwargs) for c in self.conds]
  File "/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/condition.py", line 505, in find_nuclei
    for i in range(len(self.series)))
  File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 789, in __call__
    self.retrieve()
  File "/usr/local/lib/python2.7/dist-packages/joblib/parallel.py", line 740, in retrieve
    raise exception
joblib.my_exceptions.JoblibTypeError: JoblibTypeError
___________________________________________________________________________
Multiprocessing exception:
...........................................................................
/usr/local/bin/gpseq_anim in <module>()
      1 #!/usr/bin/env python3
      2 # -*- coding: utf-8 -*-
      3 
      4 # ------------------------------------------------------------------------------
      5 # 
----> 6 # MIT License
      7 # 
      8 # Copyright (c) 2017 Gabriele Girelli
      9 # 
     10 # Permission is hereby granted, free of charge, to any person obtaining a copy

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/bin/gpseq_anim in <module>()
    383     OH.write("@%s\n\n" % datetime.datetime.now())
    384     OH.write("%s\n" % sys.version)
    385     OH.write(settings_string)
    386 
    387 # Start the analysis
--> 388 gpi = gpi.run()
    389 
    390 # End --------------------------------------------------------------------------
    391 
    392 ################################################################################

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/main.py in run(self=<pygpseq.anim.main.Main object>, **kwargs={'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'correctCA': False, 'debugging': False, 'dfield': 'lamin_dnorm', ...})
    711                 self.printout('Unskipping segmentation...', 0)
    712                 self.unskip(2)
    713         
    714         if not self.is_skipped(2):
    715             # Run segmentation if not skipped
--> 716             self.run_segmentation(**kwargs)
        self.run_segmentation = <bound method Main.run_segmentation of <pygpseq.anim.main.Main object>>
        kwargs = {'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'correctCA': False, 'debugging': False, 'dfield': 'lamin_dnorm', ...}
    717 
    718             # Dump
    719             fname = self.outdir + 'gpi.seg'+ kwargs['suffix'] +'.cpickle'
    720             f = open(fname, 'wb')

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/main.py in run_segmentation(self=<pygpseq.anim.main.Main object>, **kwargs={'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'correctCA': False, 'debugging': False, 'dfield': 'lamin_dnorm', ...})
    909         kwargs['an_type'] = self.an_type
    910 
    911         # Identify nuclei
    912         self.printout('* Looking for nuclei *', 0)
    913         self.printout('', 0)
--> 914         [c.find_nuclei(**kwargs) for c in self.conds]
        c.find_nuclei = <bound method Condition.find_nuclei of <pygpseq.anim.condition.Condition object>>
        kwargs = {'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'correctCA': False, 'debugging': False, 'dfield': 'lamin_dnorm', ...}
        c = <pygpseq.anim.condition.Condition object>
        self.conds = [<pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>, <pygpseq.anim.condition.Condition object>]
    915         self.printout('', 0)
    916 
    917     def unskip(self, step):
    918         """Unskips a run step that was supposed to be skipped. """

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/condition.py in find_nuclei(self=<pygpseq.anim.condition.Condition object>, **kwargs={'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...})
    500 
    501         # Segment every series in the condition
    502         self.printout('Current condition: "' + self.name + '"...', 0)
    503         self.series = Parallel(n_jobs = ncores)(
    504             delayed(find_series_nuclei)(self, i, **kwargs)
--> 505             for i in range(len(self.series)))
        self.series = [<pygpseq.anim.series.Series object>, <pygpseq.anim.series.Series object>, <pygpseq.anim.series.Series object>]
    506 
    507     def get_nuclei(self):
    508         """Return a list of the nuclei in the condition. """
    509         nuclei = []

...........................................................................
/usr/local/lib/python2.7/dist-packages/joblib/parallel.py in __call__(self=Parallel(n_jobs=36), iterable=<generator object <genexpr>>)
    784             if pre_dispatch == "all" or n_jobs == 1:
    785                 # The iterable was consumed all at once by the above for loop.
    786                 # No need to wait for async callbacks to trigger to
    787                 # consumption.
    788                 self._iterating = False
--> 789             self.retrieve()
        self.retrieve = <bound method Parallel.retrieve of Parallel(n_jobs=36)>
    790             # Make sure that we get a last message telling us we are done
    791             elapsed_time = time.time() - self._start_time
    792             self._print('Done %3i out of %3i | elapsed: %s finished',
    793                         (len(self._output), len(self._output),

---------------------------------------------------------------------------
Sub-process traceback:
---------------------------------------------------------------------------
TypeError                                          Mon Jun 18 20:18:22 2018
PID: 223234                               Python 2.7.15rc1: /usr/bin/python
...........................................................................
/usr/local/lib/python2.7/dist-packages/joblib/parallel.py in __call__(self=<joblib.parallel.BatchedCalls object>)
    126     def __init__(self, iterator_slice):
    127         self.items = list(iterator_slice)
    128         self._size = len(self.items)
    129 
    130     def __call__(self):
--> 131         return [func(*args, **kwargs) for func, args, kwargs in self.items]
        func = <function find_series_nuclei>
        args = (<pygpseq.anim.condition.Condition object>, 0)
        kwargs = {'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...}
        self.items = [(<function find_series_nuclei>, (<pygpseq.anim.condition.Condition object>, 0), {'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...})]
    132 
    133     def __len__(self):
    134         return self._size
    135 

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/condition.py in find_series_nuclei(self=<pygpseq.anim.condition.Condition object>, i=0, **kwargs={'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...})
    743 
    744     # Get starting time
    745     start_time = time.time()
    746 
    747     # Find nuclei
--> 748     self.series[i], log = self.series[i].find_nuclei(**kwargs)
        self.series = [<pygpseq.anim.series.Series object>, <pygpseq.anim.series.Series object>, <pygpseq.anim.series.Series object>]
        i = 0
        log = undefined
        i.find_nuclei = undefined
        kwargs = {'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...ne/IMR90_iTK226-241_080618/Data_input_iTK226_233/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...}
    749 
    750     # Print log all at once
    751     time_msg = 'Took %s s.\n' % (round(time.time() - start_time, 3))
    752     if not 1 == kwargs['ncores']:

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/anim/series.py in find_nuclei(self=<pygpseq.anim.series.Series object>, **kwargs={'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...1_080618/Data_input_iTK226_233/iTK226_070618_001/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...})
    229 
    230         # Make new channel copy
    231         i = dna_ch.copy()
    232 
    233         # Produce a mask
--> 234         Segmenter = Binarize(path = kwargs['logpath'], append = True, **kwargs)
        Segmenter = undefined
        kwargs = {'adaptive_neighbourhood': 101, 'an_type': 3, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...1_080618/Data_input_iTK226_233/iTK226_070618_001/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, 'debugging': False, ...}
    235         Segmenter.verbose = self.verbose
    236         
    237         # Check if already segmented
    238         already_segmented = False

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/tools/binarize.py in __init__(self=<pygpseq.tools.binarize.Binarize object>, **kwargs={'adaptive_neighbourhood': 101, 'an_type': 3, 'append': True, 'aspect': (300.0, 216.6, 216.6), 'basedir': '/home/bicro/Desktop/user_folders/Tomek/microscop...1_080618/Data_input_iTK226_233/iTK226_070618_001/', 'calc_n_surface': False, 'cdescr': {}, 'compressed': False, 'cond_name': 'iTK226_070618_001', 'correctCA': False, ...})
     60         """Initialize binarization settings all at once with kwargs.
     61 
     62         Args:
     63           **kwargs: arbitrary keyword arguments stored in the class.
     64         """
---> 65         super(Binarize, self).__init__()
        self.__init__ = <bound method Binarize.__init__ of <pygpseq.tools.binarize.Binarize object>>
     66 
     67         # Store provided kwargs in the current instance.
     68         excluded = ['logpath']
     69         for k in kwargs.keys():

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/tools/io.py in __init__(self=<pygpseq.tools.binarize.Binarize object>, **kwargs={})
     64                 fname, fext = os.path.splitext(curpath)
     65                 fname = fname + ' (' + str(c) + ')'
     66                 curpath = fname + fext
     67                 c += 1
     68 
---> 69         self.logpath = curpath
        self.logpath = ''
        curpath = '/tmp/pyGPSeq/log/2018-06-18_20:18:22.log'
     70     
     71     def check_log_dir(self, path = None):
     72         """Create log file directory if missing.
     73 

...........................................................................
/home/bicro/Desktop/ggcode/pygpseq/pygpseq/tools/binarize.py in __setattr__(self=<pygpseq.tools.binarize.Binarize object>, name='logpath', value='/tmp/pyGPSeq/log/2018-06-18_20:18:22.log')
     74         if key in dir(self): return(getattr(self, key))
     75         else: return(None)
     76 
     77     def __setattr__(self, name, value):
     78         """ Check the attribute and set it. """
---> 79         Binarize.check_attr(name, value)
        name = 'logpath'
        value = '/tmp/pyGPSeq/log/2018-06-18_20:18:22.log'
     80         return(super(Binarize, self).__setattr__(name, value))
     81 
     82     def __setitem__(self, key, value):
     83         """ Allow set item. """

TypeError: unbound method check_attr() must be called with Binarize instance as first argument (got str instance instead)
Additional information

My first action was to see if I am using the latest version of the pipeline. It happened to be already updated. Then, I took my previous data sets that I ran in the past and they failed at the same step. So the issue was not related to the images. I thought that maybe there was something fishy about them. Therefore, dear GG, maybe there is something silly from my side that I am doing wrong but at this point I do not know what could be the problem. Thanks! :)
ggirelli / gpseqc
