************** CELLFINDER LOG ************** Analysis carried out: 2020-12-17_17-17-01 Output directory: G:\coronal\output Current directory: C:\Users\CIBR-ImFacility-WS1 Version: 0.4.7 ************** GIT INFO ************** Gitpython is not installed. Cannot check if software is in a git repository ************** COMMAND LINE ARGUMENTS ************** Command: C:\Users\CIBR-ImFacility-WS1\anaconda3\envs\cellfinder\Scripts\cellfinder Input arguments: ['-s', 'G:\\coronal\\c0_signal', '-b', 'G:\\coronal\\c1_background', '-o', 'G:\\coronal\\output', '-v', '1', '3', '0.812', '--orientation', 'air', '--start-plane', '2000', '--end-plane', '2100', '--save-empty-cubes'] ************** VARIABLES ************** Namespace: signal_planes_paths: ['G:\\coronal\\c0_signal'] background_planes_path: ['G:\\coronal\\c1_background'] output_dir: G:\coronal\output signal_ch_ids: None background_ch_id: None registration_config: c:\users\cibr-imfacility-ws1\anaconda3\envs\cellfinder\lib\site-packages\cellfinder\config\cellfinder.conf.custom voxel_sizes: ['1', '3', '0.812'] network_voxel_sizes: [5, 1, 1] no_detection: False no_classification: False no_register: False no_analyse: False no_figures: False start_plane: 2000 end_plane: 2100 save_planes: False outlier_keep: False artifact_keep: False max_cluster_size: 100000 soma_diameter: 16 ball_xy_size: 6 ball_z_size: 15 ball_overlap_fraction: 0.6 log_sigma_size: 0.2 n_sds_above_mean_thresh: 10 soma_spread_factor: 1.4 trained_model: None model_weights: None network_depth: 50 batch_size: 32 cube_width: 50 cube_height: 50 cube_depth: 20 save_empty_cubes: True n_free_cpus: 2 max_ram: None save_csv: False debug: False sort_input_file: False no_models: False model: resnet50_tv heatmap_smooth: 100 mask_figures: True install_path: C:\Users\CIBR-ImFacility-WS1\.cellfinder download_path: C:\Users\CIBR-I~1\AppData\Local\Temp\tmp8vuonu0l no_amend_config: False atlas: allen_mouse_25um orientation: air backend: niftyreg affine_n_steps: 6 affine_use_n_steps: 5 freeform_n_steps: 6 freeform_use_n_steps: 4 bending_energy_weight: 0.95 grid_spacing: -10 smoothing_sigma_reference: -1.0 smoothing_sigma_floating: -1.0 histogram_n_bins_floating: 128 histogram_n_bins_reference: 128 Paths: output_dir: G:\coronal\output registration_output_folder: G:\coronal\output\registration metadata_path: G:\coronal\output\cellfinder.json registration_metadata_path: G:\coronal\output\registration\brainreg.json ************** LOGGING ************** 2020-12-17 17:17:01 PM - INFO - MainProcess fancylog.py:267 - Starting logging 2020-12-17 17:17:01 PM - INFO - MainProcess fancylog.py:269 - Multiprocessing-logging module found. Logging from all processes 2020-12-17 17:17:01 PM - INFO - MainProcess main.py:44 - Registering to atlas 2020-12-17 17:17:01 PM - DEBUG - MainProcess prep.py:315 - Making registration directory 2020-12-17 17:17:01 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use 2020-12-17 17:17:01 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46 2020-12-17 17:17:01 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46 2020-12-17 17:17:01 PM - INFO - MainProcess main.py:48 - Loading raw image data 2020-12-17 17:17:01 PM - DEBUG - MainProcess load.py:66 - Data type is: directory of files 2020-12-17 17:17:02 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use 2020-12-17 17:17:02 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46 2020-12-17 17:17:02 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46 2020-12-17 17:29:25 PM - INFO - MainProcess run.py:56 - Registering 2020-12-17 17:29:25 PM - INFO - MainProcess run.py:76 - Starting affine registration 2020-12-17 17:30:56 PM - INFO - MainProcess run.py:79 - Starting freeform registration 2020-12-17 17:30:58 PM - INFO - MainProcess run.py:82 - Starting segmentation 2020-12-17 17:30:59 PM - INFO - MainProcess run.py:85 - Segmenting hemispheres 2020-12-17 17:30:59 PM - INFO - MainProcess run.py:88 - Generating inverse (sample to atlas) transforms 2020-12-17 17:30:59 PM - DEBUG - MainProcess registration.py:133 - Generating inverse affine transform 2020-12-17 17:30:59 PM - DEBUG - MainProcess registration.py:170 - Registering sample to atlas 2020-12-17 17:31:03 PM - INFO - MainProcess run.py:91 - Transforming image to standard space 2020-12-17 17:31:04 PM - INFO - MainProcess run.py:97 - Generating deformation field 2020-12-17 17:31:04 PM - INFO - MainProcess registration.py:279 - Generating deformation field 2020-12-17 17:31:05 PM - INFO - MainProcess run.py:100 - Exporting images as tiff 2020-12-17 17:31:05 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI 2020-12-17 17:31:05 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1 2020-12-17 17:31:06 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI 2020-12-17 17:31:06 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1 2020-12-17 17:31:06 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI 2020-12-17 17:31:06 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1 2020-12-17 17:31:07 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI 2020-12-17 17:31:07 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1 2020-12-17 17:31:09 PM - INFO - MainProcess run.py:138 - Saving additional downsampled images 2020-12-17 17:31:09 PM - INFO - MainProcess run.py:140 - Processing: channel_0 2020-12-17 17:31:09 PM - DEBUG - MainProcess load.py:66 - Data type is: directory of files 2020-12-17 17:31:09 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use 2020-12-17 17:31:09 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46 2020-12-17 17:31:09 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46 2020-12-17 17:45:39 PM - INFO - MainProcess run.py:180 - Transforming to standard space 2020-12-17 17:45:40 PM - DEBUG - MainProcess load.py:102 - Data type is: NifTI 2020-12-17 17:45:40 PM - INFO - MainProcess batteryrunners.py:274 - pixdim[0] (qfac) should be 1 (default) or -1; setting qfac to 1 2020-12-17 17:45:41 PM - INFO - MainProcess run.py:196 - Deleting intermediate niftyreg files 2020-12-17 17:45:42 PM - INFO - MainProcess main.py:82 - Calculating volumes of each brain area 2020-12-17 17:45:42 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack 2020-12-17 17:45:42 PM - DEBUG - MainProcess load.py:149 - Loading: G:\coronal\output\registration\registered_atlas.tiff 2020-12-17 17:45:42 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack 2020-12-17 17:45:42 PM - DEBUG - MainProcess load.py:149 - Loading: G:\coronal\output\registration\registered_hemispheres.tiff 2020-12-17 17:45:43 PM - INFO - MainProcess utils.py:129 - Note: NumExpr detected 48 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. 2020-12-17 17:45:43 PM - INFO - MainProcess utils.py:141 - NumExpr defaulting to 8 threads. 2020-12-17 17:45:44 PM - WARNING - MainProcess volume.py:89 - Atlas value: 1051 not found in registered atlas. Setting registered volume to 0. 2020-12-17 17:45:44 PM - INFO - MainProcess main.py:93 - Generating boundary image 2020-12-17 17:45:44 PM - DEBUG - MainProcess load.py:90 - Data type is: tif stack 2020-12-17 17:45:44 PM - DEBUG - MainProcess load.py:149 - Loading: G:\coronal\output\registration\registered_atlas.tiff 2020-12-17 17:45:45 PM - DEBUG - MainProcess boundaries.py:22 - Saving segmentation boundary image 2020-12-17 17:45:45 PM - INFO - MainProcess main.py:100 - brainreg completed. Results can be found here: G:\coronal\output\registration 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:241 - (private) matplotlib data path: c:\users\cibr-imfacility-ws1\anaconda3\envs\cellfinder\lib\site-packages\matplotlib\mpl-data 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:241 - matplotlib data path: c:\users\cibr-imfacility-ws1\anaconda3\envs\cellfinder\lib\site-packages\matplotlib\mpl-data 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:241 - CONFIGDIR=C:\Users\CIBR-ImFacility-WS1\.matplotlib 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:1480 - matplotlib version 3.3.3 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:1481 - interactive is False 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:1482 - platform is win32 2020-12-17 17:45:45 PM - DEBUG - MainProcess __init__.py:1483 - loaded modules: ['sys', 'builtins', '_frozen_importlib', '_imp', '_thread', '_warnings', '_weakref', 'zipimport', 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'imlib.source.source_files', 'cellfinder.tools.parser', 'imlib.general.numerical', 'cellfinder.download', 'cellfinder.download.cli', 'cellfinder.download.models', 'cellfinder.download.download', 'brainreg.cli', 'brainreg.utils.misc', 'brainreg.backend.niftyreg.parser', 'brainreg.paths', 'cellfinder.tools.tf', 'tensorflow', 'tensorflow.python', 'tensorflow.python.eager', 'tensorflow.python.eager.context', 'absl', 'absl.logging', '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', 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'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.tools.tools', 'cellfinder.tools.system', 'multiprocessing_logging', 'multiprocessing.synchronize', 'ctypes.util', 'netrc', 'multiprocessing.popen_spawn_win32', 'multiprocessing.spawn', 'pandas.core.computation.expressions', 'pandas.core.computation.check', 'numexpr', 'numexpr.__config__', 'numexpr.expressions', 'numexpr.interpreter', 'numexpr.necompiler', 'numexpr.utils', 'numexpr.version', 'pandas.io.formats.csvs', 'cellfinder.detect', 'cellfinder.detect.detect', 'cellfinder.detect.filters', 'cellfinder.detect.filters.plane_filters', 'cellfinder.detect.filters.plane_filters.multiprocessing', 'cellfinder.detect.filters.plane_filters.classical_filter', 'cellfinder.detect.filters.plane_filters.tile_walker', 'cellfinder.detect.filters.plane_filters.base_tile_filter', 'cellfinder.detect.filters.setup_filters', 'cellfinder.detect.filters.volume_filters', 'cellfinder.detect.filters.volume_filters.ball_filter', 'cellfinder.tools.array_operations', 'cellfinder.tools.geometry', 'cellfinder.detect.filters.volume_filters.structure_detection', 'cellfinder.detect.filters.volume_filters.multiprocessing', 'cellfinder.detect.filters.volume_filters.structure_splitting', 'cellfinder.classify', 'cellfinder.classify.classify', 'cellfinder.classify.tools', 'cellfinder.classify.resnet', 'cellfinder.classify.cube_generator', 'skimage.io', 'skimage.io.manage_plugins', 'skimage.io.collection', 'skimage.io.sift', 'skimage.io._io', 'skimage.io.util', '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'] 2020-12-17 17:45:46 PM - DEBUG - MainProcess __init__.py:241 - CACHEDIR=C:\Users\CIBR-ImFacility-WS1\.matplotlib 2020-12-17 17:45:46 PM - DEBUG - MainProcess font_manager.py:1436 - Using fontManager instance from C:\Users\CIBR-ImFacility-WS1\.matplotlib\fontlist-v330.json 2020-12-17 17:45:46 PM - WARNING - MainProcess prep.py:271 - Registered atlas exists, assuming already run. Skipping. 2020-12-17 17:45:46 PM - INFO - MainProcess main.py:102 - Detecting cell candidates 2020-12-17 17:45:46 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use 2020-12-17 17:45:46 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46 2020-12-17 17:45:46 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46 2020-12-17 17:52:55 PM - INFO - MainProcess detect.py:141 - Detection complete - all planes done in : 0:07:09.488422 2020-12-17 17:52:55 PM - DEBUG - MainProcess system.py:134 - Determining the maximum number of CPU cores to use 2020-12-17 17:52:55 PM - DEBUG - MainProcess system.py:143 - Number of CPU cores available is: 46 2020-12-17 17:52:55 PM - DEBUG - MainProcess system.py:173 - Setting number of processes to: 46 2020-12-17 17:52:55 PM - DEBUG - MainProcess tf.py:36 - Setting maximum number of threads for tensorflow to: 46 2020-12-17 17:52:56 PM - DEBUG - MainProcess tf.py:13 - Allowing GPU memory growth 2020-12-17 17:52:57 PM - DEBUG - MainProcess tf.py:20 - 1 physical GPUs, 1 logical GPUs 2020-12-17 17:52:57 PM - DEBUG - MainProcess prep.py:355 - No model or weights supplied, so using the default 2020-12-17 17:52:57 PM - DEBUG - MainProcess prep.py:359 - Custom config does not exist, downloading models