CNMF

[whusym]

We can use CNMF to improve the performance of NMF

[melanieihuei]

CaImAn works fine but only in the specific directory
working on the reproduced-CNMF

[melanieihuei]

(environment update)

• add future package to environment.txt to make past.utils works
• do not install caiman directly from their github in case it covers those unavailable packages
• new environment set up:
  pip install -r requirements.txt
python setup.y install
• CNMFWRAP from thunder-extraction is based on CNMF from CaImAn, make sure it fits python 3.5 but not python 2.7 (map() generates iterator in py35 and reports error when importing cnmf)
• change all caiman imports to their actual path

[melanieihuei]

(running errors update)

• running CNMF from reproduced-CaImAn under caiman-env:
  errors:

  File "example_cnmf.py", line 21, in <module>
    model,temporaldata = algorithm.fit(data)
TypeError: 'CNMF' object is not iterable

• running CNMFWRAP from thunder-extraction under caiman-env:
  errors:

Traceback (most recent call last):
  File "example_cnmfwrap.py", line 13, in <module>
    model = algorithm.fit(data, chunk_size=(100,200))
  File "/Users/melanie/csci8360/p3/neurofinder.00.00/extraction/algorithms/cnmfwrap.py", line 28, in fit
    sources = asarray(blocks.map_generic(self._get))
  File "/Users/melanie/anaconda3/envs/caiman/lib/python3.5/site-packages/thunder/blocks/blocks.py", line 63, in map_generic
    return self.values.map_generic(func)[0]
  File "/Users/melanie/anaconda3/envs/caiman/lib/python3.5/site-packages/thunder/blocks/local.py", line 117, in map_generic
    arr[i] = func(x)
  File "/Users/melanie/csci8360/p3/neurofinder.00.00/extraction/algorithms/cnmfwrap.py", line 49, in _get
    model, temporaldata = algorithm.fit(block)
TypeError: 'CNMF' object is not iterable

• running CNMFWRAP from thunder-extraction under caiman-env` of neuron-example:
  errors:

RuntimeWarning: invalid value encountered in maximum
  cc = np.maximum(YrA[:, ii] + Cin[ii], -np.Inf)

[melanieihuei]

just a note for myself, im creating new environment and want to avoid those nonsense problems...

[melanieihuei]

able to run the script without having the whole repo of CaImAn (required to follow the environment setting in readme.)
need to change the neuron pixels location to neuron coordinates

[melanieihuei]

Successfully transform pixels into coordinates as required format. Implement to all the testing sets.