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abuzarmahmood / blech_clust

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Error running blech_run_process #164

Closed natashakbt closed 4 months ago

natashakbt commented 4 months ago

On commit e9a5857

Ran into an issue running bash blech_run_process.sh. Snippet of error message for electrode 5 below, but repeats the same message on about half of the electrodes. No cluster plots generated for any electrodes.

Processing electrode 5
local:6/0/100%/0.0s Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/blech_process.py", line 142, in <module>
    classifier_handler = bpu.classifier_handler(
  File "/home/natasha/Desktop/blech_clust/utils/blech_process_utils.py", line 501, in __init__
    feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/blech_process.py", line 142, in <module>
    classifier_handler = bpu.classifier_handler(
  File "/home/natasha/Desktop/blech_clust/utils/blech_process_utils.py", line 501, in __init__
    feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
local:6/0/100%/0.0s Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/blech_process.py", line 142, in <module>
    classifier_handler = bpu.classifier_handler(
  File "/home/natasha/Desktop/blech_clust/utils/blech_process_utils.py", line 501, in __init__
    feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/blech_process.py", line 142, in <module>
    classifier_handler = bpu.classifier_handler(
  File "/home/natasha/Desktop/blech_clust/utils/blech_process_utils.py", line 501, in __init__
    feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/blech_process.py", line 142, in <module>
    classifier_handler = bpu.classifier_handler(
  File "/home/natasha/Desktop/blech_clust/utils/blech_process_utils.py", line 501, in __init__
    feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/blech_process.py", line 142, in <module>
    classifier_handler = bpu.classifier_handler(
  File "/home/natasha/Desktop/blech_clust/utils/blech_process_utils.py", line 501, in __init__
    feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
local:6/0/100%/0.0s Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 81, in <module>
    ) = load_electrode_data(electrode_num) 
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in load_electrode_data
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in <listcomp>
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/anaconda3/envs/blech_clust/lib/python3.8/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: './spike_waveforms/electrode03/spike_waveforms.npy'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 81, in <module>
    ) = load_electrode_data(electrode_num) 
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in load_electrode_data
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in <listcomp>
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/anaconda3/envs/blech_clust/lib/python3.8/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: './spike_waveforms/electrode01/spike_waveforms.npy'
local:6/0/100%/0.0s Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 81, in <module>
    ) = load_electrode_data(electrode_num) 
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in load_electrode_data
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in <listcomp>
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/anaconda3/envs/blech_clust/lib/python3.8/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: './spike_waveforms/electrode05/spike_waveforms.npy'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 81, in <module>
    ) = load_electrode_data(electrode_num) 
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in load_electrode_data
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in <listcomp>
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/anaconda3/envs/blech_clust/lib/python3.8/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: './spike_waveforms/electrode02/spike_waveforms.npy'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 81, in <module>
    ) = load_electrode_data(electrode_num) 
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in load_electrode_data
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in <listcomp>
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/anaconda3/envs/blech_clust/lib/python3.8/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: './spike_waveforms/electrode04/spike_waveforms.npy'
Traceback (most recent call last):
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 81, in <module>
    ) = load_electrode_data(electrode_num) 
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in load_electrode_data
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/Desktop/blech_clust/utils/cluster_stability.py", line 38, in <listcomp>
    loaded_dat = [np.load(x) for x in loading_paths]
  File "/home/natasha/anaconda3/envs/blech_clust/lib/python3.8/site-packages/numpy/lib/npyio.py", line 416, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: './spike_waveforms/electrode00/spike_waveforms.npy'
natashakbt commented 4 months ago

Also, this is on data which I had partially analyzed but reset using python blech_clean_slate.py. Not sure if that could contribute to the error.

abuzarmahmood commented 4 months ago

It seems like your code is trying to use neurecommend functionality but can't find it. From your error snippet below:

feature_names = json.load(open(feature_names_path, 'r'))
FileNotFoundError: [Errno 2] No such file or directory: '/home/natasha/Desktop/neuRecommend/model/feature_names.json'
Traceback (most recent call last):

Under blech_clust/params/waveform_classifier _params, could you make sure that the first 3 options are set to false like below

{
   "use_neuRecommend":false,
   "use_classifier":false,
   "throw_out_noise":false,
   "min_suggestion_count" : 2000
}

Then delete results.log from the data dir and try running blech_run_process again.

If you'd like to use the classifier, that may require more setup

natashakbt commented 4 months ago

That fixed it. But got following message after rerunning and no output was generated

local:4/26/100%/3.5s Using blech_spike_features
=== Performing manual clustering ===

======================================
Classifier output not found, please run blech_run_process.sh with classifier.
======================================
abuzarmahmood commented 4 months ago

That seems to be an unresolved issue in blech_clust/utils/blech_process_utils.py check_classifier_data_exists exits if classifier data is not found, and the function is run when initializing cluster_handler. This should not be happening. You can remove the call to check_classifier_data_exists in the initialization and that should work

class cluster_handler():
    """
    Class to handle clustering steps
    """

    def __init__(self, params_dict,
                 data_dir, electrode_num, cluster_num,
                 spike_set, fit_type = 'manual'):
        assert fit_type in ['manual', 'auto'], 'fit_type must be manual or auto'
        self.check_classifier_data_exists(data_dir)
    def check_classifier_data_exists(self, data_dir):
        clf_list = glob(os.path.join(
            data_dir,
            'spike_waveforms/electrode*/clf_prob.npy'))

        if len(clf_list) == 0:
            print()
            print('======================================')
            print('Classifier output not found, please run blech_run_process.sh with classifier.')
            print('======================================')
            print()
            exit()
natashakbt commented 4 months ago

That resolved the issue, thank you!!

thomasrgray commented 3 months ago

I was encountering the same issues I tried commenting out the same line self.check_classifier_data_exists(data_dir) ( line 48 of blech_clust/utils/blech_process_utils.py) and then no plots seemed to appear. Here is the message I got 

bash blech_run_process.sh $DIR
Processing /media/thomas/Data/BackupData/TG37_active_RetEB_OrthoEB_Day4_240229_144222
Retry 1

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 2

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 3

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 4

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 5

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 6

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 7

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 8

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 9

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0
Retry 10

Computers / CPU cores / Max jobs to run
1:local / 32 / 20
0

Any advice?

abuzarmahmood commented 3 months ago

Hmm, could you run python blech_process.py $DIR 0 and tell me what you get? blech_process.py is the base script that processes the electrode so it should tell us what is happenning at the single electrode level. The error output is pretty much lost at the blech_run_process.py level.