Comments (6)
CaImAn works fine but only in the specific directory
working on the reproduced-CNMF
from johnson.
(environment update)
- add
future
package toenvironment.txt
to makepast.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
fromthunder-extraction
is based onCNMF
fromCaImAn
, make sure it fits python 3.5 but not python 2.7 (map()
generates iterator in py35 and reports error when importingcnmf
)- change all
caiman
imports to their actual path
from johnson.
(running errors update)
- running
CNMF
fromreproduced-CaImAn
undercaiman-env
:
errors:
File "example_cnmf.py", line 21, in <module>
model,temporaldata = algorithm.fit(data)
TypeError: 'CNMF' object is not iterable
- running
CNMFWRAP
fromthunder-extraction
undercaiman-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
fromthunder-extraction
under caiman-env` of neuron-example:
errors:
RuntimeWarning: invalid value encountered in maximum
cc = np.maximum(YrA[:, ii] + Cin[ii], -np.Inf)
from johnson.
just a note for myself, im creating new environment and want to avoid those nonsense problems...
from johnson.
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
from johnson.
Successfully transform pixels into coordinates as required format. Implement to all the testing sets.
from johnson.
Related Issues (14)
- Loading example.py HOT 4
- cv2 thresholds/filters HOT 2
- Unet not converging HOT 1
- Build Unet into the main file. HOT 1
- Scaling images from the results of UNet HOT 1
- Bad Unet result HOT 1
- add contributors HOT 1
- import matplotlib running on terminal HOT 6
- Having trouble accessing files on Google Cloud HOT 3
- Filtering? HOT 2
- Speeding up HOT 1
- PEP8 Standards
- I/O, prototype HOT 1
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from johnson.