Closed cindy12-gao closed 3 years ago
adamltyson
commented
3 years ago HI sorry about this. Have you recently updated cellfinder? If so, can you also update cellfinder-core (pip install cellfinder-core -U)?
If this doesn't work, could you try installing cellfinder into a new conda environment?
cindy12-gao
commented
3 years ago Hi! after updated the cellfinder-core, it can recognized the command. but there is an error, it can`t produce the ch1 file. and the error log like this.
发件人：Adam Tyson @.> 发送时间：2021年4月28日(星期三) 17:30 收件人：brainglobe/cellfinder @.> 抄 送：高辛未 @.>; Author @.> 主 题：Re: [brainglobe/cellfinder] [BUG]cellfinder training --cellfinder==0.4.12 (#174)
HI sorry about this. Have you recently updated cellfinder? If so, can you also update cellfinder-core (pip install cellfinder-core -U)? If this doesn't work, could you try installing cellfinder into a new conda environment? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.
cindy12-gao
commented
3 years ago (cellfinder) C:\Users\CIBR-ImFacility-WS2>cellfinder_train -y D:\AM_tiff\output\points\training.yml -o D:\AM_tiff\output\points --epochs 100
2021-04-28 17:46:23 PM - INFO - MainProcess fancylog.py:267 - Starting logging
2021-04-28 17:46:23 PM - INFO - MainProcess fancylog.py:269 - Multiprocessing-logging module found. Logging from all processes
2021-04-28 17:46:24 PM - DEBUG - MainProcess tpu_cluster_resolver.py:36 - Falling back to TensorFlow client; we recommended you install the Cloud TPU client directly with pip install cloud-tpu-client.
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - (private) matplotlib data path: c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\site-packages\matplotlib\mpl-data
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - matplotlib data path: c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\site-packages\matplotlib\mpl-data
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - CONFIGDIR=C:\Users\CIBR-ImFacility-WS2.matplotlib
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1480 - matplotlib version 3.3.3
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1481 - interactive is False
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1482 - platform is win32
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1483 - loaded modules: ['sys', 'builtins', '_frozen_importlib', '_imp', '_thread', '_warnings', '_weakref', 'zipimport', '_frozen_importlib_external', '_io', 'marshal', 'nt', 'winreg', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 'encodings.utf_8', '_signal', 'encodings.latin_1', 'io', 'abc', '_abc', 'site', 'os', 'stat', '_stat', '_collections_abc', 'ntpath', 'genericpath', 'os.path', '_sitebuiltins', '_bootlocale', '_locale', 'encodings.cp1252', 'types', 'importlib', 'importlib._bootstrap', 'importlib._bootstrap_external', 'warnings', 'importlib.util', 'importlib.abc', 'importlib.machinery', 'contextlib', 'collections', 'operator', '_operator', 'keyword', 'heapq', '_heapq', 'itertools', 'reprlib', '_collections', 'functools', '_functools', 'google', 'mpl_toolkits', 'sphinxcontrib', 'encodings.cp437', 'runpy', 'pkgutil', 'weakref', '_weakrefset', 'main', 're', 'enum', 'sre_compile', '_sre', 'sre_parse', 'sre_constants', 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'tensorflow.keras.applications.nasnet', 'tensorflow.keras.applications.resnet', 'tensorflow.keras.applications.resnet50', 'tensorflow.keras.applications.resnet_v2', 'tensorflow.keras.applications.vgg16', 'tensorflow.keras.applications.vgg19', 'tensorflow.keras.applications.xception', 'tensorflow.keras.backend', 'tensorflow.keras.callbacks', 'tensorflow.keras.callbacks.experimental', 'tensorflow.keras.constraints', 'tensorflow.keras.datasets', 'tensorflow.keras.datasets.boston_housing', 'tensorflow.keras.datasets.cifar10', 'tensorflow.keras.datasets.cifar100', 'tensorflow.keras.datasets.fashion_mnist', 'tensorflow.keras.datasets.imdb', 'tensorflow.keras.datasets.mnist', 'tensorflow.keras.datasets.reuters', 'tensorflow.keras.estimator', 'tensorflow.keras.experimental', 'tensorflow.keras.initializers', 'tensorflow.keras.layers', 'tensorflow.keras.layers.experimental', 'tensorflow.keras.layers.experimental.preprocessing', 'tensorflow.keras.losses', 'tensorflow.keras.metrics', 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'skimage.util._invert', 'skimage.util._montage', 'skimage.util._map_array', 'skimage.util._remap', 'skimage.data', 'skimage.data._binary_blobs', 'skimage.data._registry', 'skimage.util.lookfor', 'skimage.io', 'skimage.io.manage_plugins', 'configparser', 'skimage.io.collection', 'tifffile', 'tifffile.tifffile', 'concurrent.futures.thread', 'skimage.io.sift', 'skimage.io._io', 'skimage.color', 'skimage.color.colorconv', 'skimage.color.colorlabel', 'skimage._shared.utils', 'skimage._shared._warnings', 'skimage.color.rgb_colors', 'skimage.color.delta_e', 'skimage.io.util', 'skimage.exposure', 'skimage.exposure.exposure', 'skimage.exposure._adapthist', 'skimage.color.adapt_rgb', 'skimage.exposure.histogram_matching', 'skimage.io._image_stack', 'skimage.io._plugins', 'skimage.io._plugins.imageio_plugin', 'imageio', 'imageio.core', 'imageio.core.util', 'imageio.core.findlib', 'imageio.core.fetching', 'imageio.core.request', 'imageio.core.format', 'imageio.core.functions', 'imageio.plugins', 'imageio.plugins.tifffile', 'imageio.plugins.pillow', 'imageio.plugins.pillow_info', 'imageio.plugins.pillowmulti', 'imageio.plugins.grab', 'imageio.plugins.freeimage', 'imageio.plugins._freeimage', 'imageio.plugins.freeimagemulti', 'imageio.plugins.ffmpeg', 'imageio.plugins.bsdf', 'imageio.plugins.dicom', 'imageio.plugins.npz', 'imageio.plugins.swf', 'imageio.plugins.feisem', 'imageio.plugins.fits', 'imageio.plugins.simpleitk', 'imageio.plugins.gdal', 'imageio.plugins.lytro', 'imageio.plugins.spe', 'imageio.plugins.example', 'skimage.io._plugins.matplotlib_plugin', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axes_grid1.axes_size', 'matplotlib', 'matplotlib.cbook', 'matplotlib.cbook.deprecation', 'matplotlib.rcsetup', 'matplotlib.animation', 'matplotlib._animation_data', 'matplotlib.fontconfig_pattern', 'pyparsing', 'matplotlib.colors', 'matplotlib.docstring', 'matplotlib._color_data', 'cycler', 'matplotlib._version', 'matplotlib.ft2font', 'kiwisolver']
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - CACHEDIR=C:\Users\CIBR-ImFacility-WS2.matplotlib
2021-04-28 17:46:25 PM - DEBUG - MainProcess font_manager.py:1436 - Using fontManager instance from C:\Users\CIBR-ImFacility-WS2.matplotlib\fontlist-v330.json
2021-04-28 17:46:25 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2021-04-28 17:46:25 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46
2021-04-28 17:46:25 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46
2021-04-28 17:46:25 PM - DEBUG - MainProcess tf.py:36 - Setting maximum number of threads for tensorflow to: 46
2021-04-28 17:46:26 PM - DEBUG - MainProcess tf.py:26 - No GPUs found, using CPU.
2021-04-28 17:46:26 PM - DEBUG - MainProcess prep.py:53 - No model or weights supplied, so using the default
2021-04-28 17:46:26 PM - DEBUG - MainProcess prep.py:74 - Reading config file: c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\site-packages\cellfinder_core\config\cellfinder.conf.custom
2021-04-28 17:46:26 PM - INFO - MainProcess train_yml.py:345 - Found 155 images from 2 datasets in 1 yaml files
2021-04-28 17:46:26 PM - DEBUG - MainProcess tools.py:37 - Creating a new instance of model: 50-layer
2021-04-28 17:46:27 PM - INFO - MainProcess train_yml.py:361 - Splitting data into training and validation datasets
2021-04-28 17:46:27 PM - INFO - MainProcess train_yml.py:377 - Using 139 images for training and 16 images for validation
2021-04-28 17:46:27 PM - INFO - MainProcess train_yml.py:435 - Beginning training.
Traceback (most recent call last):
File "c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\Users\CIBR-ImFacility-WS2\Anaconda3\envs\cellfinder\Scripts\cellfinder_train.exe__main.py", line 7, in
cindy12-gao
commented
3 years ago (cellfinder) C:\Users\CIBR-ImFacility-WS2>cellfinder_train -y D:\AM_tiff\output\points\training.yml -o D:\AM_tiff\output\points --epochs 100
2021-04-28 17:46:23 PM - INFO - MainProcess fancylog.py:267 - Starting logging
2021-04-28 17:46:23 PM - INFO - MainProcess fancylog.py:269 - Multiprocessing-logging module found. Logging from all processes
2021-04-28 17:46:24 PM - DEBUG - MainProcess tpu_cluster_resolver.py:36 - Falling back to TensorFlow client; we recommended you install the Cloud TPU client directly with pip install cloud-tpu-client.
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - (private) matplotlib data path: c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\site-packages\matplotlib\mpl-data
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - matplotlib data path: c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\site-packages\matplotlib\mpl-data
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - CONFIGDIR=C:\Users\CIBR-ImFacility-WS2.matplotlib
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1480 - matplotlib version 3.3.3
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1481 - interactive is False
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1482 - platform is win32
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:1483 - loaded modules: ['sys', 'builtins', '_frozen_importlib', '_imp', '_thread', '_warnings', '_weakref', 'zipimport', '_frozen_importlib_external', '_io', 'marshal', 'nt', 'winreg', 'encodings', 'codecs', '_codecs', 'encodings.aliases', 'encodings.utf_8', '_signal', 'encodings.latin_1', 'io', 'abc', '_abc', 'site', 'os', 'stat', '_stat', '_collections_abc', 'ntpath', 'genericpath', 'os.path', '_sitebuiltins', '_bootlocale', '_locale', 'encodings.cp1252', 'types', 'importlib', 'importlib._bootstrap', 'importlib._bootstrap_external', 'warnings', 'importlib.util', 'importlib.abc', 'importlib.machinery', 'contextlib', 'collections', 'operator', '_operator', 'keyword', 'heapq', '_heapq', 'itertools', 'reprlib', '_collections', 'functools', '_functools', 'google', 'mpl_toolkits', 'sphinxcontrib', 'encodings.cp437', 'runpy', 'pkgutil', 'weakref', '_weakrefset', 'main', 're', 'enum', 'sre_compile', '_sre', 'sre_parse', 'sre_constants', 'copyreg', 'cellfinder_core', 'cellfinder_core.train', 'cellfinder_core.train.train_yml', 'logging', 'time', 'traceback', 'linecache', 'tokenize', 'token', 'collections.abc', 'string', '_string', 'threading', 'atexit', 'datetime', 'math', '_datetime', 'pathlib', 'fnmatch', 'posixpath', 'errno', 'urllib', 'urllib.parse', 'fancylog', 'fancylog.fancylog', 'fancylog.tools', 'fancylog.tools.git', 'argparse', 'gettext', 'locale', 'sklearn', 'sklearn._config', 'sklearn._distributor_init', 'ctypes', '_ctypes', 'struct', '_struct', 'ctypes._endian', 'sklearn.check_build', 'sklearn.__check_build._check_build', 'cython_runtime', 'sklearn.base', 'copy', 'platform', 'subprocess', 'signal', 'msvcrt', '_winapi', 'inspect', 'dis', 'opcode', '_opcode', 'numpy', 'numpy._globals', 'numpy.config', 'numpy.version', 'numpy._distributor_init', 'glob', 'numpy.core', 'numpy.core.multiarray', 'numpy.core.overrides', 'textwrap', 'numpy.core._multiarray_umath', 'numpy.compat', 'numpy.compat._inspect', 'numpy.compat.py3k', 'pickle', '_compat_pickle', '_pickle', 'numpy.core.umath', 'numpy.core.numerictypes', 'numbers', 'numpy.core._string_helpers', 'numpy.core._type_aliases', 'numpy.core._dtype', 'numpy.core.numeric', 'numpy.core.shape_base', 'numpy.core._asarray', 'numpy.core.fromnumeric', 'numpy.core._methods', 'numpy.core._exceptions', 'numpy.core._ufunc_config', 'numpy.core.arrayprint', 'numpy.core.defchararray', 'numpy.core.records', 'numpy.core.memmap', 'numpy.core.function_base', 'numpy.core.machar', 'numpy.core.getlimits', 'numpy.core.einsumfunc', 'numpy.core._add_newdocs', 'numpy.core._multiarray_tests', 'numpy.core._dtype_ctypes', 'numpy.core._internal', 'ast', '_ast', 'numpy._pytesttester', 'numpy.lib', 'numpy.lib.mixins', 'numpy.lib.scimath', 'numpy.lib.type_check', 'numpy.lib.ufunclike', 'numpy.lib.index_tricks', 'numpy.matrixlib', 'numpy.matrixlib.defmatrix', 'numpy.linalg', 'numpy.linalg.linalg', 'numpy.lib.twodim_base', 'numpy.linalg.lapack_lite', 'numpy.linalg._umath_linalg', 'numpy.lib.function_base', 'numpy.lib.histograms', 'numpy.lib.stride_tricks', 'numpy.lib.nanfunctions', 'numpy.lib.shape_base', 'numpy.lib.polynomial', 'numpy.lib.utils', 'numpy.lib.arraysetops', 'numpy.lib.npyio', 'numpy.lib.format', 'numpy.lib._datasource', 'shutil', 'zlib', 'bz2', '_compression', '_bz2', 'lzma', '_lzma', 'numpy.lib._iotools', 'numpy.lib.financial', 'decimal', '_decimal', 'numpy.lib.arrayterator', 'numpy.lib.arraypad', 'numpy.lib._version', 'numpy.fft', 'numpy.fft._pocketfft', 'numpy.fft._pocketfft_internal', 'numpy.fft.helper', 'numpy.polynomial', 'numpy.polynomial.polynomial', 'numpy.polynomial.polyutils', 'numpy.polynomial._polybase', 'numpy.polynomial.chebyshev', 'numpy.polynomial.legendre', 'numpy.polynomial.hermite', 'numpy.polynomial.hermite_e', 'numpy.polynomial.laguerre', 'numpy.random', 'numpy.random._pickle', 'numpy.random.mtrand', 'numpy.random.bit_generator', '_cython_0_29_21', 'numpy.random._common', 'secrets', 'base64', 'binascii', 'hmac', '_hashlib', 'hashlib', '_blake2', '_sha3', 'random', 'bisect', '_bisect', '_random', 'numpy.random._bounded_integers', 'numpy.random._mt19937', 'numpy.random._philox', 'numpy.random._pcg64', 'numpy.random._sfc64', 'numpy.random._generator', 'numpy.ctypeslib', 'numpy.ma', 'numpy.ma.core', 'numpy.ma.extras', 'sklearn.utils', 'timeit', 'gc', 'scipy', 'scipy._lib', 'scipy._lib._testutils', 'scipy._lib.deprecation', 'scipy.config', 'scipy.version', 'scipy._distributor_init', 'scipy._lib._pep440', 'scipy._lib._ccallback', 'scipy._lib._ccallback_c', 'scipy.fft', 'scipy.fft._basic', 'scipy._lib.uarray', 'scipy._lib._uarray', 'scipy._lib._uarray._backend', 'typing', 'typing.io', 'typing.re', 'scipy._lib._uarray._uarray', 'scipy.fft._realtransforms', 'scipy.fft._helper', 'scipy.fft._pocketfft', 'scipy.fft._pocketfft.basic', 'scipy.fft._pocketfft.pypocketfft', 'scipy.fft._pocketfft.helper', 'scipy.fft._pocketfft.realtransforms', 'scipy.fft._backend', 'scipy.sparse', 'scipy.sparse.base', 'scipy.sparse.sputils', 'scipy._lib._util', 'multiprocessing', 'multiprocessing.context', 'multiprocessing.process', 'multiprocessing.reduction', 'socket', '_socket', 'selectors', 'select', '__mp_main', 'scipy.sparse.csr', 'scipy.sparse._sparsetools', 'scipy.sparse.compressed', 'scipy.sparse.data', 'scipy.sparse.dia', 'scipy.sparse._index', 'scipy.sparse.csc', 'scipy.sparse.lil', 'scipy.sparse._csparsetools', 'scipy.sparse.dok', 'scipy.sparse.coo', 'scipy.sparse.bsr', 'scipy.sparse.construct', 'scipy.sparse.extract', 'scipy.sparse._matrix_io', 'scipy.sparse.csgraph', 'scipy.sparse.csgraph._laplacian', 'scipy.sparse.csgraph._shortest_path', 'scipy.sparse.csgraph._validation', 'scipy.sparse.csgraph._tools', 'scipy.sparse.csgraph._traversal', 'scipy.sparse.csgraph._min_spanning_tree', 'scipy.sparse.csgraph._flow', 'scipy.sparse.csgraph._matching', 'scipy.sparse.csgraph._reordering', 'sklearn.utils.murmurhash', 'sklearn.utils.class_weight', 'sklearn.utils.validation', 'joblib', 'joblib.memory', 'future', 'pydoc', 'sysconfig', 'joblib.hashing', 'joblib.func_inspect', 'joblib.logger', 'pprint', 'joblib.disk', 'multiprocessing.util', 'joblib._store_backends', 'json', 'json.decoder', 'json.scanner', '_json', 'json.encoder', 'joblib.backports', 'distutils', 'distutils.version', 'joblib.numpy_pickle', 'joblib.compressor', 'joblib.numpy_pickle_utils', 'joblib.numpy_pickle_compat', 'joblib.parallel', 'uuid', 'queue', '_queue', 'joblib._multiprocessing_helpers', 'tempfile', '_multiprocessing', 'joblib._parallel_backends', 'joblib.my_exceptions', 'joblib._deprecated_my_exceptions', 'joblib.pool', 'joblib._memmapping_reducer', 'mmap', 'joblib.externals', 'joblib.externals.loky', 'joblib.externals.loky._base', 'concurrent', 'concurrent.futures', 'concurrent.futures._base', 'joblib.externals.loky.backend', 'joblib.externals.loky.backend.context', 'joblib.externals.loky.backend.process', 'joblib.externals.loky.backend.compat', 'joblib.externals.loky.backend.compat_win32', 'multiprocessing.popen_spawn_win32', 'multiprocessing.spawn', 'multiprocessing.connection', 'multiprocessing.synchronize', 'joblib.externals.loky.backend.reduction', 'joblib.externals.loky.backend._win_reduction', 'joblib.externals.cloudpickle', 'joblib.externals.cloudpickle.cloudpickle', 'joblib.externals.cloudpickle.compat', 'typing_extensions', 'joblib.externals.cloudpickle.cloudpickle_fast', 'joblib.externals.loky.reusable_executor', 'joblib.externals.loky.process_executor', 'joblib.externals.loky.backend.queues', 'multiprocessing.queues', 'joblib.externals.loky.backend.utils', 'psutil', 'psutil._common', 'psutil._compat', 'psutil._pswindows', 'psutil._psutil_windows', 'concurrent.futures.process', 'joblib.externals.loky.cloudpickle_wrapper', 'joblib.externals.loky.backend.resource_tracker', 'joblib.externals.loky.backend.spawn', 'multiprocessing.pool', 'joblib.executor', 'sklearn.utils.fixes', 'scipy.stats', 'scipy.stats.stats', 'scipy.spatial', 'scipy.spatial.kdtree', 'scipy.spatial.ckdtree', 'scipy.spatial.qhull', 'scipy._lib.messagestream', 'scipy.spatial._spherical_voronoi', 'scipy.spatial._voronoi', 'scipy.spatial._plotutils', 'scipy._lib.decorator', 'scipy.spatial._procrustes', 'scipy.linalg', 'scipy.linalg.misc', 'scipy.linalg.blas', 'scipy.linalg._fblas', 'scipy.linalg.lapack', 'scipy.linalg._flapack', 'scipy.linalg.basic', 'scipy.linalg.flinalg', 'scipy.linalg._flinalg', 'scipy.linalg.decomp', 'scipy.linalg.decomp_svd', 'scipy.linalg._solve_toeplitz', 'scipy.linalg.decomp_lu', 'scipy.linalg._decomp_ldl', 'scipy.linalg.decomp_cholesky', 'scipy.linalg.decomp_qr', 'scipy.linalg._decomp_qz', 'scipy.linalg.decomp_schur', 'scipy.linalg._decomp_polar', 'scipy.linalg.matfuncs', 'scipy.linalg.special_matrices', 'scipy.linalg._expm_frechet', 'scipy.linalg._matfuncs_sqrtm', 'scipy.linalg._solvers', 'scipy.linalg._procrustes', 'scipy.linalg._decomp_update', 'scipy.linalg.cython_blas', 'scipy.linalg.cython_lapack', 'scipy.linalg._sketches', 'scipy.linalg._decomp_cossin', 'scipy.spatial._geometric_slerp', 'scipy.spatial.distance', 'scipy.spatial._distance_wrap', 'scipy.spatial._hausdorff', 'scipy.special', 'scipy.special.sf_error', 'scipy.special._ufuncs', 'scipy.special._ufuncs_cxx', 'scipy.special._basic', 'scipy.special.specfun', 'scipy.special.orthogonal', 'scipy.special._comb', 'scipy.special._logsumexp', 'scipy.special.spfun_stats', 'scipy.special._ellip_harm', 'scipy.special._ellip_harm_2', 'scipy.special._lambertw', 'scipy.special._spherical_bessel', 'scipy.spatial.transform', 'scipy.spatial.transform.rotation', 'scipy.spatial.transform._rotation_groups', 'scipy.constants', 'scipy.constants.codata', 'scipy.constants.constants', 'scipy.spatial.transform._rotation_spline', 'scipy.ndimage', 'scipy.ndimage.filters', 'scipy.ndimage._ni_support', 'scipy.ndimage._nd_image', 'scipy.ndimage._ni_docstrings', 'scipy._lib.doccer', 'scipy.ndimage.fourier', 'scipy.ndimage.interpolation', 'scipy.ndimage.measurements', 'scipy.ndimage._ni_label', '_ni_label', 'scipy.ndimage.morphology', 'scipy.stats.distributions', 'scipy.stats._distn_infrastructure', 'scipy.stats._distr_params', 'scipy.optimize', 'scipy.optimize.optimize', 'scipy.optimize.linesearch', 'scipy.optimize.minpack2', 'scipy.optimize._numdiff', 'scipy.sparse.linalg', 'scipy.sparse.linalg.isolve', 'scipy.sparse.linalg.isolve.iterative', 'scipy.sparse.linalg.isolve._iterative', 'scipy.sparse.linalg.interface', 'scipy.sparse.linalg.isolve.utils', 'scipy._lib._threadsafety', 'scipy.sparse.linalg.isolve.minres', 'scipy.sparse.linalg.isolve.lgmres', 'scipy.sparse.linalg.isolve._gcrotmk', 'scipy.sparse.linalg.isolve.lsqr', 'scipy.sparse.linalg.isolve.lsmr', 'scipy.sparse.linalg.dsolve', 'scipy.sparse.linalg.dsolve.linsolve', 'scipy.sparse.linalg.dsolve._superlu', 'scipy.sparse.linalg.dsolve._add_newdocs', 'scipy.sparse.linalg.eigen', 'scipy.sparse.linalg.eigen.arpack', 'scipy.sparse.linalg.eigen.arpack.arpack', 'scipy.sparse.linalg.eigen.arpack._arpack', 'scipy.sparse.linalg.eigen.lobpcg', 'scipy.sparse.linalg.eigen.lobpcg.lobpcg', 'scipy.sparse.linalg.matfuncs', 'scipy.sparse.linalg._expm_multiply', 'scipy.sparse.linalg._onenormest', 'scipy.sparse.linalg._norm', 'scipy.optimize._group_columns', 'scipy.optimize._differentiable_functions', 'scipy.optimize._hessian_update_strategy', 'scipy.optimize._minimize', 'scipy.optimize._trustregion_dogleg', 'scipy.optimize._trustregion', 'scipy.optimize._trustregion_ncg', 'scipy.optimize._trustregion_krylov', 'scipy.optimize._trlib', 'scipy.optimize._trlib._trlib', 'scipy.optimize._trustregion_exact', 'scipy.optimize._trustregion_constr', 'scipy.optimize._trustregion_constr.minimize_trustregion_constr', 'scipy.optimize._constraints', 'numpy.testing', 'unittest', 'unittest.result', 'unittest.util', 'unittest.case', 'difflib', 'unittest.suite', 'unittest.loader', 'unittest.main', 'unittest.runner', 'unittest.signals', 'numpy.testing._private', 'numpy.testing._private.utils', 'numpy.testing._private.decorators', 'numpy.testing._private.nosetester', 'scipy.optimize._trustregion_constr.equality_constrained_sqp', 'scipy.optimize._trustregion_constr.projections', 'scipy.optimize._trustregion_constr.qp_subproblem', 'scipy.optimize._trustregion_constr.canonical_constraint', 'scipy.optimize._trustregion_constr.tr_interior_point', 'scipy.optimize._trustregion_constr.report', 'scipy.optimize.lbfgsb', 'scipy.optimize._lbfgsb', 'scipy.optimize.tnc', 'scipy.optimize.moduleTNC', 'scipy.optimize.cobyla', 'scipy.optimize._cobyla', 'scipy.optimize.slsqp', 'scipy.optimize._slsqp', 'scipy.optimize._root', 'scipy.optimize.minpack', 'scipy.optimize._minpack', 'scipy.optimize._lsq', 'scipy.optimize._lsq.least_squares', 'scipy.optimize._lsq.trf', 'scipy.optimize._lsq.common', 'scipy.optimize._lsq.dogbox', 'scipy.optimize._lsq.lsq_linear', 'scipy.optimize._lsq.trf_linear', 'scipy.optimize._lsq.givens_elimination', 'scipy.optimize._lsq.bvls', 'scipy.optimize._spectral', 'scipy.optimize.nonlin', 'scipy.optimize._root_scalar', 'scipy.optimize.zeros', 'scipy.optimize._zeros', 'scipy.optimize._nnls', 'scipy.optimize.nnls', 'scipy.optimize._basinhopping', 'scipy.optimize._linprog', 'scipy.optimize._linprog_ip', 'scipy.optimize._linprog_util', 'scipy.optimize._remove_redundancy', 'scipy.optimize._linprog_simplex', 'scipy.optimize._linprog_rs', 'scipy.optimize._bglu_dense', 'scipy.optimize._lsap', 'scipy.optimize._lsap_module', 'scipy.optimize._differentialevolution', 'scipy.optimize._shgo', 'scipy.optimize._shgo_lib', 'scipy.optimize._shgo_lib.sobol_seq', 'scipy.optimize._shgo_lib.triangulation', 'scipy.optimize._dual_annealing', 'scipy.integrate', 'scipy.integrate._quadrature', 'scipy.integrate.odepack', 'scipy.integrate._odepack', 'scipy.integrate.quadpack', 'scipy.integrate._quadpack', 'scipy.integrate._ode', 'scipy.integrate.vode', 'scipy.integrate._dop', 'scipy.integrate.lsoda', 'scipy.integrate._bvp', 'scipy.integrate._ivp', 'scipy.integrate._ivp.ivp', 'scipy.integrate._ivp.bdf', 'scipy.integrate._ivp.common', 'scipy.integrate._ivp.base', 'scipy.integrate._ivp.radau', 'scipy.integrate._ivp.rk', 'scipy.integrate._ivp.dop853_coefficients', 'scipy.integrate._ivp.lsoda', 'scipy.integrate._quad_vec', 'scipy.misc', 'scipy.misc.doccer', 'scipy.misc.common', 'scipy.stats._constants', 'scipy.stats._continuous_distns', 'scipy.interpolate', 'scipy.interpolate.interpolate', 'scipy.interpolate.fitpack', 'scipy.interpolate._fitpack_impl', 'scipy.interpolate._fitpack', 'scipy.interpolate.dfitpack', 'scipy.interpolate._bsplines', 'scipy.interpolate._bspl', 'scipy.interpolate.polyint', 'scipy.interpolate._ppoly', 'scipy.interpolate.fitpack2', 'scipy.interpolate.interpnd', 'scipy.interpolate.rbf', 'scipy.interpolate._cubic', 'scipy.interpolate.ndgriddata', 'scipy.interpolate._pade', 'scipy.stats._stats', 'scipy.special.cython_special', 'scipy.stats._rvs_sampling', 'scipy.stats._tukeylambda_stats', 'scipy.stats._ksstats', 'scipy.stats._discrete_distns', 'scipy.stats.mstats_basic', 'scipy.stats._stats_mstats_common', 'scipy.stats._hypotests', 'scipy.stats._wilcoxon_data', 'scipy.stats.morestats', 'scipy.stats.statlib', 'scipy.stats.contingency', 'scipy.stats._binned_statistic', 'scipy.stats.kde', 'scipy.stats.mvn', 'scipy.stats.mstats', 'scipy.stats.mstats_extras', 'scipy.stats._multivariate', 'sklearn.utils.deprecation', 'pkg_resources', 'zipfile', 'plistlib', 'xml', 'xml.parsers', 'xml.parsers.expat', 'pyexpat.errors', 'pyexpat.model', 'pyexpat', 'xml.parsers.expat.model', 'xml.parsers.expat.errors', 'email', 'email.parser', 'email.feedparser', 'email.errors', 'email._policybase', 'email.header', 'email.quoprimime', 'email.base64mime', 'email.charset', 'email.encoders', 'quopri', 'email.utils', 'email._parseaddr', 'calendar', 'pkg_resources.extern', 'pkg_resources._vendor', 'pkg_resources._vendor.appdirs', 'win32com', 'win32api', 'pythoncom', 'pywintypes', 'imp', '_win32sysloader', 'win32com.gen_py', 'win32com.shell', 'pkg_resources.extern.appdirs', 'pkg_resources._vendor.packaging', 'pkg_resources._vendor.packaging.about__', 'pkg_resources.extern.packaging', 'pkg_resources.extern.packaging.version', 'pkg_resources.extern.packaging._structures', 'pkg_resources.extern.packaging._typing', 'pkg_resources.extern.packaging.specifiers', 'pkg_resources.extern.packaging._compat', 'pkg_resources.extern.packaging.utils', 'pkg_resources.extern.packaging.requirements', 'pkg_resources._vendor.pyparsing', 'pkg_resources.extern.pyparsing', 'pkg_resources.extern.packaging.markers', 'sklearn.exceptions', 'sklearn.utils._joblib', 'sklearn.utils._estimator_html_repr', 'html', 'html.entities', 'sklearn.utils._show_versions', 'sklearn.utils._openmp_helpers', 'sklearn.model_selection', 'sklearn.model_selection._split', 'sklearn.utils.multiclass', 'sklearn.model_selection._validation', 'sklearn.utils.metaestimators', 'sklearn.metrics', 'sklearn.metrics._ranking', 'sklearn.utils.extmath', 'sklearn.utils._logistic_sigmoid', 'sklearn.utils.sparsefuncs_fast', '_cython_0_29_14', 'sklearn.utils.sparsefuncs', 'sklearn.preprocessing', 'sklearn.preprocessing._function_transformer', 'sklearn.preprocessing._data', 'sklearn.preprocessing._csr_polynomial_expansion', 'sklearn.preprocessing._encoders', 'sklearn.preprocessing._label', 'array', 'sklearn.preprocessing._discretization', 'sklearn.metrics._base', 'sklearn.metrics._classification', 'sklearn.metrics.cluster', 'sklearn.metrics.cluster._supervised', 'sklearn.metrics.cluster._expected_mutual_info_fast', 'sklearn.metrics.cluster._unsupervised', 'sklearn.metrics.pairwise', 'sklearn.utils._mask', 'sklearn.metrics._pairwise_fast', 'sklearn.metrics.cluster._bicluster', 'sklearn.metrics._regression', 'sklearn._loss', 'sklearn._loss.glm_distribution', 'sklearn.metrics._scorer', 'sklearn.metrics._plot', 'sklearn.metrics._plot.roc_curve', 'sklearn.metrics._plot.base', 'sklearn.metrics._plot.precision_recall_curve', 'sklearn.metrics._plot.confusion_matrix', 'sklearn.model_selection._search', 'sklearn.utils.random', 'sklearn.utils._random', 'imlib', 'imlib.general', 'imlib.general.numerical', 'imlib.general.system', 'tqdm', 'tqdm.std', 'tqdm.utils', 'colorama', 'colorama.initialise', 'colorama.ansitowin32', 'colorama.ansi', 'colorama.winterm', 'colorama.win32', 'ctypes.wintypes', 'unicodedata', 'tqdm._monitor', 'tqdm.gui', 'tqdm._tqdm_pandas', 'tqdm.cli', 'tqdm.version', 'tqdm._dist_ver', 'slurmio', 'slurmio.slurmio', 'natsort', 'natsort.natsort', 'natsort.compat', 'natsort.compat.locale', 'natsort.utils', 'natsort.compat.fastnumbers', 'natsort.compat.fake_fastnumbers', 'natsort.unicode_numbers', 'natsort.unicode_numeric_hex', 'natsort.ns_enum', 'imlib.general.string', 'imlib.general.list', 'imlib.IO', 'imlib.IO.cells', 'yaml', 'yaml.error', 'yaml.tokens', 'yaml.events', 'yaml.nodes', 'yaml.loader', 'yaml.reader', 'yaml.scanner', 'yaml.parser', 'yaml.composer', 'yaml.constructor', 'yaml.resolver', 'yaml.dumper', 'yaml.emitter', 'yaml.serializer', 'yaml.representer', 'yaml.cyaml', '_yaml', 'pandas', 'pytz', 'pytz.exceptions', 'pytz.lazy', 'pytz.tzinfo', 'pytz.tzfile', 'dateutil', 'dateutil._version', 'pandas.compat', 'pandas._typing', 'pandas.compat.numpy', 'pandas._libs', 'pandas._libs.interval', 'pandas._libs.hashtable', 'pandas._libs.missing', 'pandas._libs.tslibs', 'pandas._libs.tslibs.dtypes', 'pandas._libs.tslibs.conversion', 'pandas._libs.tslibs.base', 'pandas._libs.tslibs.nattype', 'pandas._libs.tslibs.np_datetime', 'pandas._libs.tslibs.timezones', 'dateutil.tz', 'dateutil.tz.tz', 'six', 'six.moves', 'dateutil.tz._common', 'dateutil.tz._factories', 'dateutil.tz.win', 'pandas._libs.tslibs.tzconversion', 'pandas._libs.tslibs.ccalendar', 'pandas._libs.tslibs.parsing', 'pandas._libs.tslibs.offsets', 'pandas._libs.tslibs.timedeltas', 'pandas._libs.tslibs.timestamps', 'pandas._libs.tslibs.fields', 'pandas._config', 'pandas._config.config', 'pandas._config.dates', 'pandas._config.display', 'pandas._config.localization', 'pandas._libs.tslibs.strptime', 'dateutil.easter', 'dateutil.relativedelta', 'dateutil._common', 'pandas._libs.properties', 'dateutil.parser', 'dateutil.parser._parser', 'dateutil.parser.isoparser', 'pandas._libs.tslibs.period', 'pandas._libs.tslibs.vectorized', 'pandas._libs.ops_dispatch', 'pandas._libs.algos', 'pandas._libs.lib', 'pandas._libs.tslib', 'pandas.core', 'pandas.core.config_init', 'pandas.core.api', 'pandas.core.dtypes', 'pandas.core.dtypes.dtypes', 'pandas.core.dtypes.base', 'pandas.errors', 'pandas.core.dtypes.generic', 'pandas.core.dtypes.inference', 'pandas.core.dtypes.missing', 'pandas.core.dtypes.common', 'pandas.core.algorithms', 'pandas.util', 'pandas.util._decorators', 'pandas.core.util', 'pandas.core.util.hashing', 'pandas._libs.hashing', 'pandas.core.dtypes.cast', 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'pandas.tseries', 'pandas.tseries.frequencies', 'pandas.core.arrays._ranges', 'pandas.tseries.offsets', 'pandas.core.arrays.integer', 'pandas.core.tools', 'pandas.core.tools.numeric', 'pandas.core.arrays.interval', 'pandas.core.indexes', 'pandas.core.indexes.base', 'pandas._libs.index', 'pandas._libs.join', 'pandas.core.dtypes.concat', 'pandas.core.arrays.sparse', 'pandas.core.arrays.sparse.accessor', 'pandas.core.arrays.sparse.array', 'pandas.libs.sparse', 'pandas.core.arrays.sparse.dtype', 'pandas.io.formats.printing', 'pandas.core.indexes.frozen', 'pandas.core.strings', 'pandas.core.arrays.numpy', 'pandas.core.arrays.period', 'pandas.core.arrays.string_', 'pandas.core.arrays.timedeltas', 'pandas.core.groupby', 'pandas.core.groupby.generic', 'pandas.core.aggregation', 'pandas.core.indexes.api', 'pandas.core.indexes.category', 'pandas.core.indexes.extension', 'pandas.core.indexes.datetimes', 'pandas.core.indexes.datetimelike', 'pandas.core.indexes.numeric', 'pandas.core.tools.timedeltas', 'pandas.core.tools.times', 'pandas.core.indexes.interval', 'pandas.util._exceptions', 'pandas.core.indexes.multi', 'pandas.core.indexes.timedeltas', 'pandas.core.indexes.period', 'pandas.core.indexes.range', 'pandas.core.series', 'pandas._libs.reshape', 'pandas.core.generic', 'pandas.core.indexing', 'pandas._libs.indexing', 'pandas.core.internals', 'pandas.core.internals.blocks', 'pandas._libs.writers', 'pandas._libs.internals', 'pandas.core.internals.concat', 'pandas.core.internals.managers', 'pandas.core.internals.ops', 'pandas.core.shared_docs', 'pandas.io.formats.format', 'pandas.io.common', 'gzip', 'pandas.core.indexes.accessors', 'pandas.core.tools.datetimes', 'pandas.arrays', 'pandas.plotting', 'pandas.plotting._core', 'pandas.plotting._misc', 'pandas.core.window', 'pandas.core.window.ewm', 'pandas._libs.window', 'pandas.libs.window.aggregations', 'pandas.core.window.common', 'pandas.core.groupby.base', 'pandas.core.window.rolling', 'pandas.core.util.numba', 'pandas.core.window.indexers', 'pandas.libs.window.indexers', 'pandas.core.window.numba', 'pandas.core.window.expanding', 'pandas.core.frame', 'pandas.core.internals.construction', 'pandas.core.reshape', 'pandas.core.reshape.melt', 'pandas.core.reshape.concat', 'pandas.core.reshape.util', 'pandas.io.formats.info', 'pandas.core.groupby.groupby', 'pandas._libs.groupby', 'pandas.core.groupby.ops', 'pandas._libs.reduction', 'pandas.core.groupby.grouper', 'pandas.core.groupby.categorical', 'pandas.tseries.api', 'pandas.core.computation', 'pandas.core.computation.api', 'pandas.core.computation.eval', 'pandas.core.computation.engines', 'pandas.core.computation.align', 'pandas.core.computation.common', 'pandas.core.computation.ops', 'pandas.core.computation.scope', 'pandas.compat.chainmap', 'pandas.core.computation.expr', 'pandas.core.computation.parsing', 'pandas.core.reshape.api', 'pandas.core.reshape.merge', 'pandas.core.reshape.pivot', 'pandas.core.reshape.reshape', 'pandas.core.reshape.tile', 'pandas.api', 'pandas.api.extensions', 'pandas.api.indexers', 'pandas.api.types', 'pandas.core.dtypes.api', 'pandas.util._print_versions', 'pandas.io.api', 'pandas.io.clipboards', 'pandas.io.excel', 'pandas.io.excel._base', 'pandas._libs.parsers', 'pandas.io.excel._util', 'pandas.io.parsers', 'pandas.io.date_converters', 'pandas.io.excel._odfreader', 'pandas.io.excel._openpyxl', 'pandas.io.excel._pyxlsb', 'pandas.io.excel._xlrd', 'pandas.io.excel._odswriter', 'pandas._libs.json', 'pandas.io.formats.excel', 'pandas.io.formats.css', 'pandas.io.excel._xlsxwriter', 'pandas.io.excel._xlwt', 'pandas.io.feather_format', 'pandas.io.gbq', 'pandas.io.html', 'pandas.io.json', 'pandas.io.json._json', 'pandas.io.json._normalize', 'pandas.io.json._table_schema', 'pandas.io.orc', 'pandas.io.parquet', 'pandas.io.pickle', 'pandas.compat.pickle_compat', 'pandas.io.pytables', 'pandas.core.computation.pytables', 'pandas.io.sas', 'pandas.io.sas.sasreader', 'pandas.io.spss', 'pandas.io.sql', 'pandas.io.stata', 'pandas.util._tester', 'pandas.testing', 'pandas._testing', 'pandas._libs.testing', 'pandas._version', 'xml.dom', 'xml.dom.domreg', 'xml.dom.minidom', 'xml.dom.minicompat', 'xml.dom.xmlbuilder', 'xml.dom.NodeFilter', 'xml.etree', 'xml.etree.ElementTree', 'xml.etree.ElementPath', '_elementtree', 'imlib.cells', 'imlib.cells.cells', 'imlib.IO.yaml', 'cellfinder_core.download', 'cellfinder_core.download.cli', 'cellfinder_core.download.models', 'cellfinder_core.download.download', 'tarfile', 'urllib.request', 'http', 'http.client', 'email.message', 'uu', 'email._encoded_words', 'email.iterators', 'ssl', '_ssl', 'urllib.error', 'urllib.response', 'nturl2path', 'imlib.general.config', 'configobj', '_version', 'cellfinder_core.tools', 'cellfinder_core.tools.source_files', 'multiprocessing_logging', 'cellfinder_core.main', 'imlib.general.logging', 'tensorflow', 'tensorflow.python', 'tensorflow.python.pywrap_tensorflow', 'tensorflow.python.platform', 'tensorflow.python.platform.self_check', 'tensorflow.python.platform.build_info', 'tensorflow.python.pywrap_dlopen_global_flags', 'tensorflow.python._pywrap_tensorflow_internal', 'tensorflow.python.eager', 'tensorflow.python.eager.context', 'absl', 'absl.logging', 'getpass', 'absl.flags', 'getopt', 'absl.flags._argument_parser', 'absl.flags._helpers', 'absl.flags._defines', 'absl.flags._exceptions', 'absl.flags._flag', 'absl._collections_abc', 'absl.flags._flagvalues', 'absl.flags._validators', 'absl.logging.converter', 'tensorflow.core', 'tensorflow.core.framework', 'tensorflow.core.framework.function_pb2', 'google.protobuf', 'google.protobuf.descriptor', 'google.protobuf.internal', 'google.protobuf.internal.api_implementation', 'google.protobuf.internal._api_implementation', 'google.protobuf.pyext', 'google.protobuf.internal.containers', 'google.protobuf.internal.enum_type_wrapper', 'google.protobuf.message', 'google.protobuf.pyext._message', 'google.protobuf.reflection', 'google.protobuf.message_factory', 'google.protobuf.descriptor_pool', 'google.protobuf.descriptor_database', 'google.protobuf.text_encoding', 'google.protobuf.pyext.cpp_message', 'google.protobuf.symbol_database', 'tensorflow.core.framework.attr_value_pb2', 'tensorflow.core.framework.tensor_pb2', 'tensorflow.core.framework.resource_handle_pb2', 'tensorflow.core.framework.tensor_shape_pb2', 'google.protobuf.internal.well_known_types', 'tensorflow.core.framework.types_pb2', 'tensorflow.core.framework.node_def_pb2', 'tensorflow.core.framework.op_def_pb2', 'tensorflow.core.protobuf', 'tensorflow.core.protobuf.config_pb2', 'tensorflow.core.framework.cost_graph_pb2', 'tensorflow.core.framework.graph_pb2', 'tensorflow.core.framework.versions_pb2', 'tensorflow.core.framework.step_stats_pb2', 'tensorflow.core.framework.allocation_description_pb2', 'tensorflow.core.framework.tensor_description_pb2', 'tensorflow.core.protobuf.cluster_pb2', 'tensorflow.core.protobuf.debug_pb2', 'tensorflow.core.protobuf.rewriter_config_pb2', 'tensorflow.core.protobuf.verifier_config_pb2', 'tensorflow.python.pywrap_tfe', 'tensorflow.python._pywrap_tfe', 'tensorflow.python.tf2', 'tensorflow.python.client', 'tensorflow.python.client.pywrap_tf_session', 'tensorflow.python._pywrap_tf_session', 'tensorflow.python.eager.executor', 'tensorflow.python.eager.monitoring', 'tensorflow.core.framework.summary_pb2', 'tensorflow.python.framework', 'tensorflow.python.framework.c_api_util', 'tensorflow.core.framework.api_def_pb2', 'tensorflow.python.util', 'tensorflow.python.util.compat', 'tensorflow.python.util.tf_export', 'tensorflow.python.util.tf_decorator', 'tensorflow.python.util.tf_stack', 'tensorflow.python._tf_stack', 'tensorflow.python.util.tf_inspect', 'tensorflow.python.util.tf_contextlib', 'tensorflow.python.framework.device', 'tensorflow.python.framework.device_spec', 'tensorflow.python.framework.tfrt_utils', 'tensorflow.python.util.is_in_graph_mode', 'tensorflow.python.util.deprecation', 'tensorflow.python.platform.tf_logging', 'tensorflow.python.util.decorator_utils', 'tensorflow.tools', 'tensorflow.tools.docs', 'tensorflow.tools.docs.doc_controls', 'tensorflow.python.data', 'tensorflow.python.data.experimental', 'tensorflow.python.data.experimental.service', 'tensorflow.python.data.experimental.ops', 'tensorflow.python.data.experimental.ops.data_service_ops', 'tensorflow.python.data.experimental.ops.compression_ops', 'tensorflow.python.data.util', 'tensorflow.python.data.util.structure', 'wrapt', 'wrapt.wrappers', 'wrapt.decorators', 'wrapt.importer', 'tensorflow.python.data.util.nest', 'tensorflow.python._pywrap_utils', 'tensorflow.python.framework.sparse_tensor', 'tensorflow.python.framework.composite_tensor', 'tensorflow.python.util.nest', 'tensorflow.python.framework.constant_op', 'tensorflow.python.eager.execute', 'google.protobuf.text_format', 'encodings.raw_unicode_escape', 'encodings.unicode_escape', 'google.protobuf.internal.decoder', 'google.protobuf.internal.encoder', 'google.protobuf.internal.wire_format', 'google.protobuf.internal.type_checkers', 'tensorflow.python.eager.core', 'tensorflow.python.framework.errors', 'tensorflow.python.framework.errors_impl', 'tensorflow.core.lib', 'tensorflow.core.lib.core', 'tensorflow.core.lib.core.error_codes_pb2', 'tensorflow.core.protobuf.error_codes_pb2', 'tensorflow.python._pywrap_py_exception_registry', 'tensorflow.python.framework.error_interpolation', 'tensorflow.core.protobuf.graph_debug_info_pb2', 'tensorflow.python.framework.dtypes', 'tensorflow.python._pywrap_bfloat16', 'tensorflow.python._dtypes', 'tensorflow.python.framework.ops', 'tensorflow.python.eager.tape', 'tensorflow.python.util.lazy_loader', 'tensorflow.python.framework.indexed_slices', 'tensorflow.python.framework.tensor_conversion_registry', 'tensorflow.python.framework.tensor_shape', 'tensorflow.python.framework.type_spec', 'tensorflow.python.types', 'tensorflow.python.types.internal', 'tensorflow.python.framework.registry', 'tensorflow.python.framework.traceable_stack', 'tensorflow.python.framework.versions', 'tensorflow.python.ops', 'tensorflow.python.ops.control_flow_util', 'tensorflow.python.platform.app', 'absl.app', 'pdb', 'cmd', 'bdb', 'code', 'codeop', 'absl.command_name', 'faulthandler', 'tensorflow.python.platform.flags', 'tensorflow.python.profiler', 'tensorflow.python.profiler.trace', 'tensorflow.python.profiler.internal', 'tensorflow.python.profiler.internal._pywrap_traceme', 'tensorflow.python.types.core', 'tensorflow.python.types.doc_typealias', 'tensorflow.python.util.dispatch', 'tensorflow.python.util.function_utils', 'tensorflow.python.util.lock_util', 'tensorflow.python.util.memory', 'tensorflow.python.util.object_identity', 'tensorflow.python.framework.op_callbacks', 'tensorflow.python.framework.tensor_util', 'tensorflow.python.framework.tensor_spec', 'tensorflow.python.framework.common_shapes', 'tensorflow.python.ops.gen_sparse_ops', 'tensorflow.python.framework.op_def_registry', 'tensorflow.python._op_def_registry', 'tensorflow.python.framework.op_def_library', 'tensorflow.python.ops.tensor_array_ops', 'tensorflow.python.ops.array_ops', 'tensorflow.python.ops.gen_array_ops', 'tensorflow.python.ops.gen_math_ops', 'tensorflow.python.ops.gen_control_flow_ops', 'tensorflow.python.ops.gen_data_flow_ops', 'tensorflow.python.ops.list_ops', 'tensorflow.python.framework.cpp_shape_inference_pb2', 'tensorflow.python.ops.gen_list_ops', 'tensorflow.python.ops.handle_data_util', 'tensorflow.python.ops.math_ops', 'tensorflow.python.framework.graph_util', 'tensorflow.python.framework.graph_util_impl', 'tensorflow.python.ops.gen_bitwise_ops', 'tensorflow.python.ops.gen_nn_ops', 'tensorflow.python.util.tf_should_use', 'tensorflow.python.ops.ragged', 'tensorflow.python.ops.ragged.ragged_tensor', 'tensorflow.python.client.session', 'tensorflow.python.ops.session_ops', 'tensorflow.python.training', 'tensorflow.python.training.experimental', 'tensorflow.python.training.experimental.mixed_precision_global_state', 'tensorflow.python.ops.check_ops', 'tensorflow.python.ops.control_flow_ops', 'tensorflow.core.protobuf.control_flow_pb2', 'tensorflow.python.ops.gen_functional_ops', 'tensorflow.python.ops.gen_logging_ops', 'tensorflow.python.ops.gen_ragged_conversion_ops', 'tensorflow.python.ops.ragged.ragged_config', 'tensorflow.python.ops.ragged.ragged_tensor_value', 'tensorflow.python.ops.ragged.ragged_util', 'tensorflow.python.ops.gen_ragged_math_ops', 'tensorflow.python.ops.ragged.row_partition', 'tensorflow.python.ops.ragged.segment_id_ops', 'tensorflow.python.ops.gen_experimental_dataset_ops', 'tensorflow.python.data.experimental.ops.distribute_options', 'tensorflow.python.data.util.options', 'tensorflow.python.data.ops', 'tensorflow.python.data.ops.dataset_ops', 'tensorflow.python.data.experimental.ops.optimization_options', 'tensorflow.python.data.experimental.ops.stats_options', 'tensorflow.python.data.experimental.ops.stats_aggregator', 'tensorflow.python.ops.summary_ops_v2', 'tensorflow.python.eager.profiler', 'tensorflow.python._pywrap_events_writer', 'tensorflow.python.platform.gfile', 'tensorflow.python.lib', 'tensorflow.python.lib.io', 'tensorflow.python.lib.io.file_io', 'tensorflow.python._pywrap_file_io', 'tensorflow.python.profiler.internal._pywrap_profiler', 'tensorflow.python.framework.smart_cond', 'tensorflow.python.ops.gen_summary_ops', 'tensorflow.python.ops.resource_variable_ops', 'tensorflow.core.framework.variable_pb2', 'tensorflow.python.framework.auto_control_deps_utils', 'tensorflow.python.ops.gen_resource_variable_ops', 'tensorflow.python.ops.gen_state_ops', 'tensorflow.python.ops.state_ops', 'tensorflow.python.ops.variables', 'tensorflow.python.training.tracking', 'tensorflow.python.training.tracking.base', 'tensorflow.python.ops.gen_io_ops', 'tensorflow.python.training.saving', 'tensorflow.python.training.saving.saveable_object', 'tensorflow.python.ops.summary_op_util', 'tensorflow.python.training.training_util', 'tensorflow.python.framework.graph_io', 'tensorflow.python.ops.init_ops', 'tensorflow.python.ops.gen_linalg_ops', 'tensorflow.python.ops.linalg_ops_impl', 'tensorflow.python.ops.random_ops', 'tensorflow.python.framework.random_seed', 'tensorflow.python.ops.gen_random_ops', 'tensorflow.python.ops.stateless_random_ops', 'tensorflow.python.compat', 'tensorflow.python.compat.compat', 'tensorflow.python.ops.gen_stateless_random_ops', 'tensorflow.python.ops.gen_stateless_random_ops_v2', 'tensorflow.python.ops.variable_scope', 'tensorflow.python.data.experimental.ops.threading_options', 'tensorflow.python.data.ops.iterator_ops', 'tensorflow.python.data.ops.optional_ops', 'tensorflow.python.ops.gen_dataset_ops', 'tensorflow.python.training.saver', 'tensorflow.core.protobuf.meta_graph_pb2', 'google.protobuf.any_pb2', 'tensorflow.core.protobuf.saved_object_graph_pb2', 'tensorflow.core.protobuf.struct_pb2', 'tensorflow.core.protobuf.trackable_object_graph_pb2', 'tensorflow.core.protobuf.saver_pb2', 'tensorflow.python.framework.meta_graph', 'tensorflow.python.framework.importer', 'tensorflow.python.framework.function', 'tensorflow.python.framework.graph_to_function_def', 'tensorflow.python.ops.io_ops', 'tensorflow.python.lib.io.python_io', 'tensorflow.python.lib.io.tf_record', 'tensorflow.python._pywrap_record_io', 'tensorflow.python.ops.string_ops', 'tensorflow.python.ops.gen_parsing_ops', 'tensorflow.python.ops.gen_string_ops', 'tensorflow.python.training.checkpoint_management', 'tensorflow.python.training.checkpoint_state_pb2', 'tensorflow.python.training.py_checkpoint_reader', 'tensorflow.python._pywrap_checkpoint_reader', 'tensorflow.python.training.saving.saveable_object_util', 'tensorflow.python.eager.def_function', 'tensorflow.python.distribute', 'tensorflow.python.distribute.parallel_device', 'tensorflow.python.distribute.parallel_device.parallel_device', 'tensorflow.python._pywrap_parallel_device', 'tensorflow.python.distribute.device_util', 'tensorflow.python.framework.config', 'tensorflow.python._pywrap_tensor_float_32_execution', 'tensorflow.python.distribute.parallel_device.saving', 'tensorflow.python.tpu', 'tensorflow.python.tpu.ops', 'tensorflow.python.tpu.ops.tpu_ops', 'tensorflow.python.ops.gen_tpu_ops', 'tensorflow.python.tpu.tpu_function', 'tensorflow.python.eager.function', 'tensorflow.python.eager.backprop', 'tensorflow.python.eager.backprop_util', 'tensorflow.python.eager.imperative_grad', 'tensorflow.python.ops.unconnected_gradients', 'tensorflow.python.ops.default_gradient', 'tensorflow.python.eager.forwardprop_util', 'tensorflow.python.eager.graph_only_ops', 'tensorflow.python.framework.func_graph', 'tensorflow.python.framework.auto_control_deps', 'tensorflow.python.ops.custom_gradient', 'tensorflow.python.ops.op_selector', 'tensorflow.python.ops.functional_ops', 'tensorflow.python.ops.gradients_util', 'tensorflow.python.ops.control_flow_state', 'tensorflow.python.ops.control_flow_v2_func_graphs', 'tensorflow.python.saved_model', 'tensorflow.python.saved_model.save_context', 'tensorflow.python.eager.lift_to_graph', 'tensorflow.python.data.util.convert', 'tensorflow.python.data.util.random_seed', 'tensorflow.python.data.util.traverse', 'tensorflow.python.ops.script_ops', 'tensorflow.python._pywrap_py_func', 'tensorflow.python.ops.gen_script_ops', 'tensorflow.python.training.tracking.tracking', 'tensorflow.python.training.tracking.data_structures', 'tensorflow.python.saved_model.revived_types', 'tensorflow.python.training.tracking.layer_utils', 'tensorflow.python.data.experimental.service.server_lib', 'tensorflow.core.protobuf.data', 'tensorflow.core.protobuf.data.experimental', 'tensorflow.core.protobuf.data.experimental.service_config_pb2', 'tensorflow.python.data.experimental.service._pywrap_server_lib', 'tensorflow.python.data.experimental.ops.batching', 'tensorflow.python.data.experimental.ops.cardinality', 'tensorflow.python.data.experimental.ops.counter', 'tensorflow.python.data.experimental.ops.scan_ops', 'tensorflow.python.data.experimental.ops.enumerate_ops', 'tensorflow.python.data.experimental.ops.error_ops', 'tensorflow.python.data.experimental.ops.get_single_element', 'tensorflow.python.data.experimental.ops.grouping', 'tensorflow.python.data.experimental.ops.interleave_ops', 'tensorflow.python.data.experimental.ops.random_ops', 'tensorflow.python.data.ops.readers', 'tensorflow.python.data.experimental.ops.io', 'tensorflow.python.data.experimental.ops.iterator_ops', 'tensorflow.python.training.basic_session_run_hooks', 'tensorflow.core.util', 'tensorflow.core.util.event_pb2', 'tensorflow.python.client.timeline', 'tensorflow.python.training.session_run_hook', 'tensorflow.python.training.summary_io', 'tensorflow.python.summary', 'tensorflow.python.summary.summary_iterator', 'tensorflow.python.summary.writer', 'tensorflow.python.summary.writer.writer', 'tensorflow.python.summary.plugin_asset', 'tensorflow.python.summary.writer.event_file_writer', 'tensorflow.python.summary.writer.event_file_writer_v2', 'tensorflow.python.summary.writer.writer_cache', 'tensorflow.python.data.experimental.ops.parsing_ops', 'tensorflow.python.ops.parsing_ops', 'tensorflow.python.ops.parsing_config', 'tensorflow.python.ops.sparse_ops', 'tensorflow.python.ops.special_math_ops', 'opt_einsum', 'opt_einsum.blas', 'opt_einsum.helpers', 'opt_einsum.parser', 'opt_einsum.paths', 'opt_einsum.path_random', 'opt_einsum.contract', 'opt_einsum.backends', 'opt_einsum.backends.cupy', 'opt_einsum.sharing', 'opt_einsum.backends.dispatch', 'opt_einsum.backends.object_arrays', 'opt_einsum.backends.jax', 'opt_einsum.backends.tensorflow', 'opt_einsum.backends.theano', 'opt_einsum.backends.torch', 'opt_einsum._version', 'tensorflow.compiler', 'tensorflow.compiler.tf2xla', 'tensorflow.compiler.tf2xla.ops', 'tensorflow.compiler.tf2xla.ops.gen_xla_ops', 'tensorflow.python.ops.gen_special_math_ops', 'tensorflow.python.ops.ragged.ragged_math_ops', 'tensorflow.python.ops.ragged.ragged_functional_ops', 'tensorflow.python.data.experimental.ops.prefetching_ops', 'tensorflow.python.data.experimental.ops.readers', 'tensorflow.python.data.experimental.ops.resampling', 'tensorflow.python.ops.logging_ops', 'tensorflow.python.data.experimental.ops.shuffle_ops', 'tensorflow.python.data.experimental.ops.snapshot', 'tensorflow.python.data.experimental.ops.stats_ops', 'tensorflow.python.data.experimental.ops.take_while_ops', 'tensorflow.python.data.experimental.ops.unique', 'tensorflow.python.data.experimental.ops.writers', 'tensorflow.python.util.all_util', 'tensorflow.python.keras', 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'tensorflow.keras.applications.nasnet', 'tensorflow.keras.applications.resnet', 'tensorflow.keras.applications.resnet50', 'tensorflow.keras.applications.resnet_v2', 'tensorflow.keras.applications.vgg16', 'tensorflow.keras.applications.vgg19', 'tensorflow.keras.applications.xception', 'tensorflow.keras.backend', 'tensorflow.keras.callbacks', 'tensorflow.keras.callbacks.experimental', 'tensorflow.keras.constraints', 'tensorflow.keras.datasets', 'tensorflow.keras.datasets.boston_housing', 'tensorflow.keras.datasets.cifar10', 'tensorflow.keras.datasets.cifar100', 'tensorflow.keras.datasets.fashion_mnist', 'tensorflow.keras.datasets.imdb', 'tensorflow.keras.datasets.mnist', 'tensorflow.keras.datasets.reuters', 'tensorflow.keras.estimator', 'tensorflow.keras.experimental', 'tensorflow.keras.initializers', 'tensorflow.keras.layers', 'tensorflow.keras.layers.experimental', 'tensorflow.keras.layers.experimental.preprocessing', 'tensorflow.keras.losses', 'tensorflow.keras.metrics', 'tensorflow.keras.mixed_precision', 'tensorflow.keras.mixed_precision.experimental', 'tensorflow.keras.models', 'tensorflow.keras.optimizers', 'tensorflow.keras.optimizers.schedules', 'tensorflow.keras.preprocessing', 'tensorflow.keras.preprocessing.image', 'tensorflow.keras.preprocessing.sequence', 'tensorflow.keras.preprocessing.text', 'tensorflow.keras.regularizers', 'tensorflow.keras.utils', 'tensorflow.keras.wrappers', 'tensorflow.keras.wrappers.scikit_learn', 'cellfinder_core.tools.prep', 'cellfinder_core.tools.tf', 'cellfinder_core.classify', 'cellfinder_core.classify.tools', 'cellfinder_core.classify.resnet', 'cellfinder_core.classify.cube_generator', 'skimage', 'skimage._shared', 'skimage._shared.version_requirements', 'skimage._shared.geometry', 'skimage.util', 'skimage.util.dtype', 'skimage.util.shape', 'skimage.util.noise', 'skimage.util.apply_parallel', 'skimage.util.arraycrop', 'skimage.util.compare', 'skimage.util._regular_grid', 'skimage.util.unique', 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'imageio.plugins.tifffile', 'imageio.plugins.pillow', 'imageio.plugins.pillow_info', 'imageio.plugins.pillowmulti', 'imageio.plugins.grab', 'imageio.plugins.freeimage', 'imageio.plugins._freeimage', 'imageio.plugins.freeimagemulti', 'imageio.plugins.ffmpeg', 'imageio.plugins.bsdf', 'imageio.plugins.dicom', 'imageio.plugins.npz', 'imageio.plugins.swf', 'imageio.plugins.feisem', 'imageio.plugins.fits', 'imageio.plugins.simpleitk', 'imageio.plugins.gdal', 'imageio.plugins.lytro', 'imageio.plugins.spe', 'imageio.plugins.example', 'skimage.io._plugins.matplotlib_plugin', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axes_grid1.axes_size', 'matplotlib', 'matplotlib.cbook', 'matplotlib.cbook.deprecation', 'matplotlib.rcsetup', 'matplotlib.animation', 'matplotlib._animation_data', 'matplotlib.fontconfig_pattern', 'pyparsing', 'matplotlib.colors', 'matplotlib.docstring', 'matplotlib._color_data', 'cycler', 'matplotlib._version', 'matplotlib.ft2font', 'kiwisolver']
2021-04-28 17:46:25 PM - DEBUG - MainProcess init.py:241 - CACHEDIR=C:\Users\CIBR-ImFacility-WS2.matplotlib
2021-04-28 17:46:25 PM - DEBUG - MainProcess font_manager.py:1436 - Using fontManager instance from C:\Users\CIBR-ImFacility-WS2.matplotlib\fontlist-v330.json
2021-04-28 17:46:25 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use
2021-04-28 17:46:25 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46
2021-04-28 17:46:25 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46
2021-04-28 17:46:25 PM - DEBUG - MainProcess tf.py:36 - Setting maximum number of threads for tensorflow to: 46
2021-04-28 17:46:26 PM - DEBUG - MainProcess tf.py:26 - No GPUs found, using CPU.
2021-04-28 17:46:26 PM - DEBUG - MainProcess prep.py:53 - No model or weights supplied, so using the default
2021-04-28 17:46:26 PM - DEBUG - MainProcess prep.py:74 - Reading config file: c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\site-packages\cellfinder_core\config\cellfinder.conf.custom
2021-04-28 17:46:26 PM - INFO - MainProcess train_yml.py:345 - Found 155 images from 2 datasets in 1 yaml files
2021-04-28 17:46:26 PM - DEBUG - MainProcess tools.py:37 - Creating a new instance of model: 50-layer
2021-04-28 17:46:27 PM - INFO - MainProcess train_yml.py:361 - Splitting data into training and validation datasets
2021-04-28 17:46:27 PM - INFO - MainProcess train_yml.py:377 - Using 139 images for training and 16 images for validation
2021-04-28 17:46:27 PM - INFO - MainProcess train_yml.py:435 - Beginning training.
Traceback (most recent call last):
File "c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "c:\users\cibr-imfacility-ws2\anaconda3\envs\cellfinder\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\Users\CIBR-ImFacility-WS2\Anaconda3\envs\cellfinder\Scripts\cellfinder_train.exe__main.py", line 7, in
adamltyson
commented
3 years ago The training script is trying to find files in this directory D:\AM_tiff\output\points\non_cells. Is this directory accessible on your computer? Have you moved the training data, or the yml file?
cindy12-gao
commented
3 years ago no, I didnt move any files. but there are none of 'ch1'files in the non-cells folder, and all of them are 'ch0' files.so whats the definition of the 'ch1' files ? thank you
adamltyson
commented
3 years ago The ch1 files are the background channel, (ch0 is the signal channel), so there's something wrong with the training data. Do you have any other training data you could test with?
cindy12-gao
commented
3 years ago maybe I know whats the problem. Actually, I have two signal channels without reference channel, one of them has few signal point, so I pretend this channel to the background channel, Im not sure whether it work.
adamltyson
commented
3 years ago It may not work very well, but it shouldn't cause this bug. Have you managed to train the network with another training dataset?
adamltyson
commented
3 years ago Are you still having this problem?
cindy12-gao
commented
3 years ago I reinstalled the version 0.4.13 rc0, now it can run.
adamltyson
commented
3 years ago Great, thanks for letting me know. The final 0.4.13 release should be soon.
cindy12-gao
commented
3 years ago sorry for the unclearly express, I mean after installed the rc version, there is no error like unrecognized the cellfinder command,but the cellfinder_train still has the error message like I mentioned above
adamltyson
commented
3 years ago Have you managed to train with another dataset?
cindy12-gao
commented
3 years ago do you mean the other raw data or different slices of the same brain dataset?
cindy12-gao
commented
3 years ago actually I`ve known the reason why it failed. the background and the signal file number are different. sorry about my carelessness
Describe the bug when I entered the command 'cellfinder_train -y D:\AM_tiff\output\points\training.yml -o D:\AM_tiff\output\points' there is an error ''cellfinder_train' is not recognized as an internal or external command, operable program or batch file.'
I`ve used the cellfinder_curate to produce the .yml profile, so the error like this is so weird. now the version of cellfinder is 0.4.12. hope for your answer. thank you!
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