Tight Annotation Analysis on the collman15v2 data

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import importlib 
import numpy as np
import toolbox
import annoTightAll
import h5py
importlib.reload(toolbox)
importlib.reload(annoTightAll)


    

    
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<module 'annoTightAll' from '/Users/JLP/neurodata-dev/synaptome-stats/collman15v2/201710/annoTightAll.py'>

In [5]:

    

COLL_NAME      = 'collman' 
EXP_NAME       = 'collman15v2' 
ANNO_NAME      = 'annotation' 
COORD_FRAME    = 'collman_collman15v2'
CONFIG_FILE    = 'config.ini'
OUTPUT         = 'test20171211.csv'

CHAN_NAMES = ['DAPI1st', 'DAPI2nd', 'DAPI3rd', 'GABA488', 'GAD647',
        'gephyrin594', 'GS594', 'MBP488', 'NR1594', 'PSD95_488',
        'Synapsin647', 'VGluT1_647']


    

In [6]:

    

cubes, loc, F0, nonzeros, ids = annoTightAll.main(COLL_NAME, EXP_NAME, COORD_FRAME,
     CHAN_NAMES=CHAN_NAMES, ANNO_NAME = ANNO_NAME, num_threads = 6, CONFIG_FILE= 'config.ini')


    

    




---------------------------------------------------------------------------
HTTPError                                 Traceback (most recent call last)
<ipython-input-6-a68d6b8ec646> in <module>()
      1 cubes, loc, F0, nonzeros, ids = annoTightAll.main(COLL_NAME, EXP_NAME, COORD_FRAME,
----> 2      CHAN_NAMES=CHAN_NAMES, ANNO_NAME = ANNO_NAME, num_threads = 6, CONFIG_FILE= 'config.ini')

~/neurodata-dev/synaptome-stats/collman15v2/201710/annoTightAll.py in main(COLL_NAME, EXP_NAME, COORD_FRAME, CHAN_NAMES, ANNO_NAME, num_threads, CONFIG_FILE)
     44 
     45     cf = CoordinateFrameResource(str(COLL_NAME + '_' + EXP_NAME))
---> 46     cfr = rem.get_project(cf)
     47     anno_res = ChannelResource(ANNO_NAME, COLL_NAME, EXP_NAME, 'annotation', datatype='uint64')
     48 

/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/intern/remote/boss/remote.py in get_project(self, resource)
    717         """
    718         self.project_service.set_auth(self._token_project)
--> 719         return self.project_service.get(resource)
    720 
    721     def update_project(self, resource_name, resource):

/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/intern/service/boss/project.py in get(self, resource)
    432         return self.service.get(
    433             resource, self.url_prefix, self.auth, self.session,
--> 434             self.session_send_opts)
    435 
    436     def update(self, resource_name, resource):

/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/intern/service/boss/v1/project.py in get(self, resource, url_prefix, auth, session, send_opts)
    792         err = ('Get failed on {}, got HTTP response: ({}) - {}'.format(
    793             resource.name, resp.status_code, resp.text))
--> 794         raise HTTPError(err, request = req, response = resp)
    795 
    796     def update(self, resource_name, resource, url_prefix, auth, session, send_opts):

HTTPError: Get failed on collman_collman15v2, got HTTP response: (500) - <h1>Server Error (500)</h1>

In [4]:

    

F0w = np.divide(F0, nonzeros)


    

In [5]:

    

toolbox.mainOUT(F0w, CHAN_NAMES, OUTPUT)


    

In [6]:

    

#toolbox.toh5(EXP_NAME, OUTPUT + '.h5', CHAN_NAMES, cubes, loc)


    

In [12]:

    

toolbox.mainOUT(np.transpose(loc), ['z','y','x'], 'locations' + OUTPUT)


    

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