def hash(self):
return mt.sha1OfObject(
dict(name='downsampled-recording-extractor',
version=2,
recording=self._recording.hash(),
ds_factor=self._ds_factor,
input_has_minmax=self._input_has_minmax))
def _samplehash(recording):
from mountaintools import client as mt
obj = {
'channels': tuple(recording.get_channel_ids()),
'frames': recording.get_num_frames(),
'data': _samplehash_helper(recording)
}
return mt.sha1OfObject(obj)
def hash(self):
from mountainclient import client as mt
obj = dict(
raw=mt.computeFileSha1(self._timeseries_path),
geom=mt.computeFileSha1(self._geom_fname),
params=self._dataset_params
)
return mt.sha1OfObject(obj)
def _samplehash(sorting):
from mountaintools import client as mt
obj = {
'unit_ids': sorting.get_unit_ids(),
'sampling_frequency': sorting.get_sampling_frequency(),
'data': _samplehash_helper(sorting)
}
return mt.sha1OfObject(obj)
def hash(self):
params = self.paramsForHash() # pylint: disable=assignment-from-none
if params is None:
raise Exception('Cannot compute hash. Params for hash not implemented.')
return mt.sha1OfObject(dict(
name='FilterRecording',
params=params,
recording=self._recording.hash()
))
def install_waveclus(repo, commit):
spikeforest_alg_install_path = get_install_path()
key = dict(
alg='waveclus',
repo=repo,
commit=commit
)
source_path = spikeforest_alg_install_path + '/waveclus_' + commit
if os.path.exists(source_path):
# The dir hash method does not seem to be working for some reason here
# hash0 = mt.computeDirHash(source_path)
# if hash0 == mt.getValue(key=key):
# print('waveclus is already auto-installed.')
# return source_path
a = mt.loadObject(path=source_path + '/spikeforest.json')
if a:
if mt.sha1OfObject(a) == mt.sha1OfObject(key):
print('waveclus is already auto-installed.')
return source_path
print('Removing directory: {}'.format(source_path))
shutil.rmtree(source_path)
script = """
#!/bin/bash
set -e
git clone {repo} {source_path}
cd {source_path}
git checkout {commit}
""".format(repo=repo, commit=commit, source_path=source_path)
ss = mlpr.ShellScript(script=script)
ss.start()
retcode = ss.wait()
if retcode != 0:
raise Exception('Install script returned a non-zero exit code/')
# The dir hash method does not seem to be working for some reason here
# hash0 = mt.computeDirHash(source_path)
# mt.setValue(key=key, value=hash0)
mt.saveObject(object=key, dest_path=source_path + '/spikeforest.json')
return source_path
def hash(self):
if not self._recording_hash:
if hasattr(self._recording, 'hash'):
if type(self._recording.hash) == str:
self._recording_hash = self._recording.hash
else:
self._recording_hash = self._recording.hash()
else:
self._recording_hash = _samplehash(self._recording)
return mt.sha1OfObject(
dict(name='downsampled-recording-extractor',
version=2,
recording=self._recording_hash,
ds_factor=self._ds_factor,
input_has_minmax=self._input_has_minmax))
def install_jrclust(repo, commit):
spikeforest_alg_install_path = get_install_path()
key = dict(alg='jrclust', repo=repo, commit=commit)
source_path = spikeforest_alg_install_path + '/jrclust_' + commit
if os.path.exists(source_path):
# The dir hash method does not seem to be working for some reason here
# hash0 = mt.computeDirHash(source_path)
# if hash0 == mt.getValue(key=key):
# print('jrclust is already auto-installed.')
# return source_path
a = mt.loadObject(path=source_path + '/spikeforest.json')
if a:
if mt.sha1OfObject(a) == mt.sha1OfObject(key):
print('jrclust is already auto-installed.')
return source_path
print('Removing directory: {}'.format(source_path))
shutil.rmtree(source_path)
script = """
#!/bin/bash
set -e
git clone {repo} {source_path}
cd {source_path}
git checkout {commit}
""".format(repo=repo, commit=commit, source_path=source_path)
ss = mlpr.ShellScript(script=script)
ss.start()
retcode = ss.wait()
if retcode != 0:
raise Exception('Install script returned a non-zero exit code/')
compile_gpu = mlpr.ShellScript(script="""
function compile_gpu
try
jrc compile
catch
disp('Problem running `jrc compile`');
disp(lasterr());
exit(-1)
end;
exit(0)
""")
compile_gpu.write(script_path=source_path + '/compile_gpu.m')
script = """
#!/bin/bash
set -e
cd {source_path}
matlab -nodisplay -nosplash -r "compile_gpu"
""".format(source_path=source_path)
ss = mlpr.ShellScript(script=script)
ss.start()
retcode = ss.wait()
if retcode != 0:
raise Exception('Compute gpu script returned a non-zero exit code.')
# The dir hash method does not seem to be working for some reason here
# hash0 = mt.computeDirHash(source_path)
# mt.setValue(key=key, value=hash0)
mt.saveObject(object=key, dest_path=source_path + '/spikeforest.json')
return source_path
def install_kilosort2(repo, commit):
spikeforest_alg_install_path = get_install_path()
key = dict(alg='kilosort2', repo=repo, commit=commit)
source_path = spikeforest_alg_install_path + '/kilosort2_' + commit
if os.path.exists(source_path):
# The dir hash method does not seem to be working for some reason here
# hash0 = mt.computeDirHash(source_path)
# if hash0 == mt.getValue(key=key):
# print('Kilosort2 is already auto-installed.')
# return source_path
a = mt.loadObject(path=source_path + '/spikeforest.json')
if a:
if mt.sha1OfObject(a) == mt.sha1OfObject(key):
print('Kilosort2 is already auto-installed.')
return source_path
print('Removing directory: {}'.format(source_path))
shutil.rmtree(source_path)
script = """
#!/bin/bash
set -e
git clone {repo} {source_path}
cd {source_path}
git checkout {commit}
""".format(repo=repo, commit=commit, source_path=source_path)
ss = mlpr.ShellScript(script=script)
ss.start()
retcode = ss.wait()
if retcode != 0:
raise Exception('Install script returned a non-zero exit code/')
# make sure module unload gcc/7.4.0
compile_gpu = mlpr.ShellScript(script="""
function compile_gpu
try
[~,path_nvcc_] = system('which nvcc');
path_nvcc_ = strrep(path_nvcc_, 'nvcc', '');
disp(['path_nvcc_: ', path_nvcc_]);
setenv('MW_NVCC_PATH', path_nvcc_);
run('mexGPUall.m');
catch
disp('Problem running mexGPUall.');
disp(lasterr());
exit(-1)
end;
exit(0)
""")
compile_gpu.write(script_path=source_path + '/CUDA/compile_gpu.m')
script = """
#!/bin/bash
set -e
cd {source_path}/CUDA
matlab -nodisplay -nosplash -r "compile_gpu"
""".format(source_path=source_path)
ss = mlpr.ShellScript(script=script)
ss.start()
retcode = ss.wait()
if retcode != 0:
raise Exception('Compute gpu script returned a non-zero exit code.')
# The dir hash method does not seem to be working for some reason here
# hash0 = mt.computeDirHash(source_path)
# mt.setValue(key=key, value=hash0)
mt.saveObject(object=key, dest_path=source_path + '/spikeforest.json')
return source_path