diff --git a/config_fatma_gevi_M0134M_SessionA2_Test.json b/config_fatma_gevi_M0134M_SessionA2_Test.json new file mode 100644 index 0000000..b1d0f83 --- /dev/null +++ b/config_fatma_gevi_M0134M_SessionA2_Test.json @@ -0,0 +1,61 @@ +{ + "basic_path": "/data_1/fatma/GEVI", + "recoding_data": "2024-10-16", + "mouse_identifier": "M0134M_SessionA2_Test", + "export_path": "output_2024-10-16_M0134M_SessionA2_Test", + "ref_image_path": "ref_images_2024-10-16_M0134M_SessionA2_Test", + "raw_path": "raw", + "heartbeat_remove": true, // if gevi must be true; geci: who knows... + "gevi": true, // true => gevi, false => geci + // Ratio Sequence + "classical_ratio_mode": true, // true: a/d false: 1+a-d + // Regression + "target_camera_acceptor": "acceptor", + "regressor_cameras_acceptor": [ + "oxygenation", + "volume" + ], + "target_camera_donor": "donor", + "regressor_cameras_donor": [ + "oxygenation", + "volume" + ], + // binning + "binning_enable": true, + "binning_at_the_end": false, + "binning_kernel_size": 4, + "binning_stride": 4, + "binning_divisor_override": 1, + // alignment + "alignment_batch_size": 200, + "rotation_stabilization_threshold_factor": 3.0, // >= 1.0 + "rotation_stabilization_threshold_border": 0.9, // <= 1.0 + // Heart beat detection + "lower_freqency_bandpass": 5.0, // Hz + "upper_freqency_bandpass": 14.0, // Hz + "heartbeat_filtfilt_chuck_size": 10, + // Gauss smear + "gauss_smear_spatial_width": 8, + "gauss_smear_temporal_width": 0.1, + "gauss_smear_use_matlab_mask": false, + // LED Ramp on + "skip_frames_in_the_beginning": 100, // Frames + // PyTorch + "dtype": "float32", + "force_to_cpu": false, + // Save + "save_as_python": true, // produces .npz files (compressed) + "save_as_matlab": false, // produces .hd5 file (compressed) + // Save extra information + "save_alignment": false, + "save_heartbeat": false, + "save_factors": false, + "save_regression_coefficients": false, + // Not important parameter + "required_order": [ + "acceptor", + "donor", + "oxygenation", + "volume" + ] +} diff --git a/stage_5_convert_metadata.py b/stage_5_convert_metadata.py index 1e5e7c2..31e1ce2 100644 --- a/stage_5_convert_metadata.py +++ b/stage_5_convert_metadata.py @@ -6,7 +6,9 @@ from functions.get_trials import get_trials from functions.get_experiments import get_experiments -def converter(filename: str = "config_M_Sert_Cre_49.json") -> None: +def converter(config_filename: str = "config.json") -> None: + + filename: str = config_filename if os.path.isfile(filename) is False: print(f"{filename} is missing") diff --git a/stage_6_convert_roi.py b/stage_6_convert_roi.py index 34dbe33..18176db 100644 --- a/stage_6_convert_roi.py +++ b/stage_6_convert_roi.py @@ -6,7 +6,9 @@ import numpy as np import h5py -def converter(filename: str = "config_M_Sert_Cre_49.json") -> None: +def converter(config_filename: str = "config.json") -> None: + + filename: str = config_filename if os.path.isfile(filename) is False: print(f"{filename} is missing")