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Update stage_5_convert_metadata.py
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2025-08-03 01:00:02 +02:00 · 2025-03-19 18:36:14 +01:00 · 2025-03-19 18:35:14 +01:00 · 2025-03-19 18:34:08 +01:00 · 2025-03-19 18:32:36 +01:00 · 2025-03-19 18:32:03 +01:00
29 changed files with 942 additions and 64 deletions
--- a/README.md
+++ b/README.md
@ -11,3 +11,49 @@ Ruhr-Universität Bochum, Universitätsbibliothek
 08.02.2024

 [https://doi.org/10.13154/294-11032](https://doi.org/10.13154/294-11032)
+
+-----------------------------------------------------------------------------------------------------
+
+Updated: 19.03.2025
+
+Files are now organized in subdirectories to distinguish better between code for GEVI or GECI analysis.
+```
+gevi-geci/
+    stage_1*, stage_2*, stage_3*, stage_4*, stage_5*
+	-> main stages for data preprocessing
+	-> use e.g.: python stage_1_get_ref_image.py -c config_example_GEVI.json
+    functions/
+	-> functions used by the main stages
+	
+gevi-geci/gevi/
+    config_example_GEVI.json
+    	-> typical config file for GEVI (compare to gevi-geci/geci/config_example_GECI.json)
+    config_M0134M*, config_M3905F*
+	-> config files for a few recordings (adjust directory names, if necessary!)
+    example_load_gevi.py
+	-> simple script demonstrating how to load data
+
+gevi-geci/geci/
+    config_example_GECI.json
+	-> typical config file for GECI (compare to gevi-geci/gevi/config_example_GEVI.json)
+    config_M_Sert_Cre_4*
+	-> config files for a few recordings (adjust directory names, if necessary!)
+    stage_6_convert_roi.py
+	-> additional stage for the analysis of Hendrik's recordings
+	-> use e.g.: python stage_6_convert_roi.py -f config_M_Sert_Cre_41.json 
+    geci_loader.py, geci_plot.py
+	-> additional code for summarizing the results and plotting with the ROIs
+	-> use e.g. python geci_loader.py --filename config_M_Sert_Cre_41.json
+	
+gevi-geci/other/
+    stage_4b_inspect.py, stage_4c_viewer.py
+	-> temporary code for assisting search for implantation electrode
+```	
+
+    
+
+
+
+
+
+
--- a/geci/config_M_Sert_Cre_41.json
+++ b/geci/config_M_Sert_Cre_41.json
@ -3,14 +3,14 @@
    "recoding_data": "2023-07-17",
    "mouse_identifier": "M_Sert_Cre_41",
    "raw_path": "raw",
-    "export_path": "output_M_Sert_Cre_41",
-    "ref_image_path": "ref_images_M_Sert_Cre_41",
-    "heartbeat_remove": false,
-    "gevi": false, // true => gevi, false => geci
+    "export_path": "output/M_Sert_Cre_41",
+    "ref_image_path": "ref_images/M_Sert_Cre_41",
+	"heartbeat_remove": true,
+	"gevi": false, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
-    //"target_camera_acceptor": "acceptor",
+    // EMPTY FOR GECI   "target_camera_acceptor": "acceptor",
    "target_camera_acceptor": "",
    "regressor_cameras_acceptor": [
        "oxygenation",
@ -18,7 +18,7 @@
    ],
    "target_camera_donor": "donor",
    "regressor_cameras_donor": [
-        //    "oxygenation",
+        // REMOVED FOR GECI   "oxygenation",
        "volume"
    ],
    // binning
@ -52,6 +52,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
@ -59,4 +64,4 @@
        "oxygenation",
        "volume"
    ]
-}
+}
--- a/geci/config_M_Sert_Cre_42.json
+++ b/geci/config_M_Sert_Cre_42.json
@ -3,14 +3,14 @@
    "recoding_data": "2023-07-18",
    "mouse_identifier": "M_Sert_Cre_42",
    "raw_path": "raw",
-    "export_path": "output_M_Sert_Cre_42",
-    "ref_image_path": "ref_images_M_Sert_Cre_42",
-    "heartbeat_remove": false,
-    "gevi": false, // true => gevi, false => geci
+    "export_path": "output/M_Sert_Cre_42",
+    "ref_image_path": "ref_images/M_Sert_Cre_42",
+	"heartbeat_remove": true,
+	"gevi": false, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
-    //"target_camera_acceptor": "acceptor",
+    // EMPTY FOR GECI   "target_camera_acceptor": "acceptor",
    "target_camera_acceptor": "",
    "regressor_cameras_acceptor": [
        "oxygenation",
@ -18,7 +18,7 @@
    ],
    "target_camera_donor": "donor",
    "regressor_cameras_donor": [
-        //    "oxygenation",
+        // REMOVED FOR GECI   "oxygenation",
        "volume"
    ],
    // binning
@ -52,6 +52,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/geci/config_M_Sert_Cre_45.json
+++ b/geci/config_M_Sert_Cre_45.json
@ -3,14 +3,14 @@
    "recoding_data": "2023-07-18",
    "mouse_identifier": "M_Sert_Cre_45",
    "raw_path": "raw",
-    "export_path": "output_M_Sert_Cre_45",
-    "ref_image_path": "ref_images_M_Sert_Cre_45",
-    "heartbeat_remove": false,
-    "gevi": false, // true => gevi, false => geci
+    "export_path": "output/M_Sert_Cre_45",
+    "ref_image_path": "ref_images/M_Sert_Cre_45",
+	"heartbeat_remove": true,
+	"gevi": false, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
-    //"target_camera_acceptor": "acceptor",
+    // EMPTY FOR GECI   "target_camera_acceptor": "acceptor",
    "target_camera_acceptor": "",
    "regressor_cameras_acceptor": [
        "oxygenation",
@ -18,7 +18,7 @@
    ],
    "target_camera_donor": "donor",
    "regressor_cameras_donor": [
-        //    "oxygenation",
+        // REMOVED FOR GECI   "oxygenation",
        "volume"
    ],
    // binning
@ -52,6 +52,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/geci/config_M_Sert_Cre_46.json
+++ b/geci/config_M_Sert_Cre_46.json
@ -3,14 +3,14 @@
    "recoding_data": "2023-03-16",
    "mouse_identifier": "M_Sert_Cre_46",
    "raw_path": "raw",
-    "export_path": "output_M_Sert_Cre_46",
-    "ref_image_path": "ref_images_M_Sert_Cre_46",
-    "heartbeat_remove": false,
-    "gevi": false, // true => gevi, false => geci
+    "export_path": "output/M_Sert_Cre_46",
+    "ref_image_path": "ref_images/M_Sert_Cre_46",
+	"heartbeat_remove": true,
+	"gevi": false, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
-    //"target_camera_acceptor": "acceptor",
+    // EMPTY FOR GECI   "target_camera_acceptor": "acceptor",
    "target_camera_acceptor": "",
    "regressor_cameras_acceptor": [
        "oxygenation",
@ -18,7 +18,7 @@
    ],
    "target_camera_donor": "donor",
    "regressor_cameras_donor": [
-        //    "oxygenation",
+        // REMOVED FOR GECI   "oxygenation",
        "volume"
    ],
    // binning
@ -52,6 +52,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/geci/config_M_Sert_Cre_49.json
+++ b/geci/config_M_Sert_Cre_49.json
@ -3,14 +3,14 @@
    "recoding_data": "2023-03-15",
    "mouse_identifier": "M_Sert_Cre_49",
    "raw_path": "raw",
-    "export_path": "output_M_Sert_Cre_49",
-    "ref_image_path": "ref_images_M_Sert_Cre_49",
-    "heartbeat_remove": false,
-    "gevi": false, // true => gevi, false => geci
+    "export_path": "output/M_Sert_Cre_49",
+    "ref_image_path": "ref_images/M_Sert_Cre_49",
+	"heartbeat_remove": true,
+	"gevi": false, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
-    //"target_camera_acceptor": "acceptor",
+    // EMPTY FOR GECI   "target_camera_acceptor": "acceptor",
    "target_camera_acceptor": "",
    "regressor_cameras_acceptor": [
        "oxygenation",
@ -18,7 +18,7 @@
    ],
    "target_camera_donor": "donor",
    "regressor_cameras_donor": [
-        //    "oxygenation",
+        // REMOVED FOR GECI   "oxygenation",
        "volume"
    ],
    // binning
@ -52,6 +52,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
@ -59,4 +64,4 @@
        "oxygenation",
        "volume"
    ]
-}
+}
--- a/geci/config_example_GECI.json
+++ b/geci/config_example_GECI.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/hendrik",
+    "recoding_data": "2023-07-17",
+    "mouse_identifier": "M_Sert_Cre_41",
+    "raw_path": "raw",
+    "export_path": "output/M_Sert_Cre_41",
+    "ref_image_path": "ref_images/M_Sert_Cre_41",
+	"heartbeat_remove": true,
+	"gevi": false, // true => gevi, false => geci
+    // Ratio Sequence
+    "classical_ratio_mode": true, // true: a/d false: 1+a-d
+    // Regression
+    // EMPTY FOR GECI   "target_camera_acceptor": "acceptor",
+    "target_camera_acceptor": "",
+    "regressor_cameras_acceptor": [
+        "oxygenation",
+        "volume"
+    ],
+    "target_camera_donor": "donor",
+    "regressor_cameras_donor": [
+        // REMOVED FOR GECI   "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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/geci/geci_loader.py
+++ b/geci/geci_loader.py
--- a/geci/geci_plot.py
+++ b/geci/geci_plot.py
--- a/geci/stage_6_convert_roi.py
+++ b/geci/stage_6_convert_roi.py
@ -6,9 +6,7 @@ import numpy as np
 import h5py


-def converter(config_filename: str = "config.json") -> None:
-
-    filename: str = config_filename
+def converter(filename: str = "config_M_Sert_Cre_49.json") -> None:

    if os.path.isfile(filename) is False:
        print(f"{filename} is missing")
@ -37,7 +35,7 @@ def converter(config_filename: str = "config.json") -> None:
    if os.path.isfile(roi_control_mat):
        hf = h5py.File(roi_control_mat, "r")
        roi_control = np.array(hf["roi"]).T
-        filename_out: str = f"roi_control{config["mouse_identifier"]}.npy"
+        filename_out: str = f"roi_control{config['mouse_identifier']}.npy"
        np.save(filename_out, roi_control)
    else:
        print("ROI Control not found")
@ -45,7 +43,7 @@ def converter(config_filename: str = "config.json") -> None:
    if os.path.isfile(roi_sdarken_mat):
        hf = h5py.File(roi_sdarken_mat, "r")
        roi_darken = np.array(hf["roi"]).T
-        filename_out = f"roi_sdarken{config["mouse_identifier"]}.npy"
+        filename_out: str = f"roi_sdarken{config['mouse_identifier']}.npy"
        np.save(filename_out, roi_darken)
    else:
        print("ROI sDarken not found")
--- a/config_fatma_gevi_M0134M_SessionA2_Test.json
+++ b/config_fatma_gevi_M0134M_SessionA2_Test.json
@ -1,12 +1,13 @@
 {
-    "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",
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-06",
+    "mouse_identifier": "M0134M_SessionA",
    "raw_path": "raw",
-    "heartbeat_remove": true, // if gevi must be true; geci: who knows...
-    "gevi": true, // true => gevi, false => geci
+    "export_path": "output/M0134M_2024-11-06_SessionA",
+    "ref_image_path": "ref_images/M0134M_2024-11-06_SessionA",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"gevi": true, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
@ -51,6 +52,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/gevi/config_M0134M_2024-11-06_SessionB.json
+++ b/gevi/config_M0134M_2024-11-06_SessionB.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-06",
+    "mouse_identifier": "M0134M_SessionB",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-06_SessionB",
+    "ref_image_path": "ref_images/M0134M_2024-11-06_SessionB",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-07_SessionA.json
+++ b/gevi/config_M0134M_2024-11-07_SessionA.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-07",
+    "mouse_identifier": "M0134M_SessionA",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-07_SessionA",
+    "ref_image_path": "ref_images/M0134M_2024-11-07_SessionA",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-07_SessionB.json
+++ b/gevi/config_M0134M_2024-11-07_SessionB.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-07",
+    "mouse_identifier": "M0134M_SessionB",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-07_SessionB",
+    "ref_image_path": "ref_images/M0134M_2024-11-07_SessionB",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-13_SessionA.json
+++ b/gevi/config_M0134M_2024-11-13_SessionA.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-13",
+    "mouse_identifier": "M0134M_SessionA",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-13_SessionA",
+    "ref_image_path": "ref_images/M0134M_2024-11-13_SessionA",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-13_SessionB.json
+++ b/gevi/config_M0134M_2024-11-13_SessionB.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-13",
+    "mouse_identifier": "M0134M_SessionB",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-13_SessionB",
+    "ref_image_path": "ref_images/M0134M_2024-11-13_SessionB",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-15_SessionA.json
+++ b/gevi/config_M0134M_2024-11-15_SessionA.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-15",
+    "mouse_identifier": "M0134M_SessionA",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-15_SessionA",
+    "ref_image_path": "ref_images/M0134M_2024-11-15_SessionA",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-15_SessionB.json
+++ b/gevi/config_M0134M_2024-11-15_SessionB.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-15",
+    "mouse_identifier": "M0134M_SessionB",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-15_SessionB",
+    "ref_image_path": "ref_images/M0134M_2024-11-15_SessionB",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-11-18_SessionA.json
+++ b/gevi/config_M0134M_2024-11-18_SessionA.json
@ -3,8 +3,8 @@
    "recoding_data": "2024-11-18",
    "mouse_identifier": "M0134M_SessionA",
    "raw_path": "raw",
-    "export_path": "output_M0134M_SessionA",
-    "ref_image_path": "ref_images_M0134M_SessionA",
+    "export_path": "output/M0134M_2024-11-18_SessionA",
+    "ref_image_path": "ref_images/M0134M_2024-11-18_SessionA",
 	"raw_path": "raw",
 	"heartbeat_remove": true,
 	"gevi": true, // true => gevi, false => geci
@ -56,6 +56,7 @@
 	"save_aligned_as_matlab": false,
 	"save_oxyvol_as_python": false,
 	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/gevi/config_M0134M_2024-11-18_SessionB.json
+++ b/gevi/config_M0134M_2024-11-18_SessionB.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-11-18",
+    "mouse_identifier": "M0134M_SessionB",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-11-18_SessionB",
+    "ref_image_path": "ref_images/M0134M_2024-11-18_SessionB",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-12-04_SessionA.json
+++ b/gevi/config_M0134M_2024-12-04_SessionA.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-12-04",
+    "mouse_identifier": "M0134M_SessionA",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-12-04_SessionA",
+    "ref_image_path": "ref_images/M0134M_2024-12-04_SessionA",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M0134M_2024-12-04_SessionB.json
+++ b/gevi/config_M0134M_2024-12-04_SessionB.json
@ -0,0 +1,67 @@
+{
+    "basic_path": "/data_1/fatma/GEVI/",
+    "recoding_data": "2024-12-04",
+    "mouse_identifier": "M0134M_SessionB",
+    "raw_path": "raw",
+    "export_path": "output/M0134M_2024-12-04_SessionB",
+    "ref_image_path": "ref_images/M0134M_2024-12-04_SessionB",
+	"raw_path": "raw",
+	"heartbeat_remove": true,
+	"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,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
+    // Not important parameter
+    "required_order": [
+        "acceptor",
+        "donor",
+        "oxygenation",
+        "volume"
+    ]
+}
--- a/gevi/config_M3905F_SessionB.json
+++ b/gevi/config_M3905F_SessionB.json
@ -3,8 +3,8 @@
    "recoding_data": "session_B",
    "mouse_identifier": "M3905F",
    "raw_path": "raw",
-    "export_path": "output_M3905F_session_B",
-    "ref_image_path": "ref_images_M3905F_session_B",
+    "export_path": "output/M3905F_SessionB",
+    "ref_image_path": "ref_images/M3905F_SessionB",
 	"raw_path": "raw",
 	"heartbeat_remove": true,
 	"gevi": true, // true => gevi, false => geci
@ -54,8 +54,9 @@
    "save_regression_coefficients": false,
 	"save_aligned_as_python": false,
 	"save_aligned_as_matlab": false,
-	"save_oxyvol_as_python": true,
-	"save_oxyvol_as_matlab": true,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/gevi/config_example_GEVI.json
+++ b/gevi/config_example_GEVI.json
@ -1,12 +1,12 @@
 {
-    "basic_path": "/data_1/robert",
-    "recoding_data": "2021-10-05",
-    "mouse_identifier": "M3879M",
+    "basic_path": "/data_1/fatma/GEVI_GECI_ES",
+    "recoding_data": "session_B",
+    "mouse_identifier": "M3905F",
    "raw_path": "raw",
-    "export_path": "output_M3879M_2021-10-05",
-    "ref_image_path": "ref_images_M3879M_2021-10-05",
-    "heartbeat_remove": true, // if gevi must be true; geci: who knows...
-    "gevi": true, // true => gevi, false => geci
+    "export_path": "output/M3905F_SessionB",
+    "ref_image_path": "ref_images/M3905F_SessionB",
+	"heartbeat_remove": true,
+	"gevi": true, // true => gevi, false => geci
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
@ -51,6 +51,11 @@
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
+	"save_aligned_as_python": false,
+	"save_aligned_as_matlab": false,
+	"save_oxyvol_as_python": false,
+	"save_oxyvol_as_matlab": false,
+    "save_gevi_with_donor_acceptor": true,
    // Not important parameter
    "required_order": [
        "acceptor",
--- a/gevi/example_load_gevi.py
+++ b/gevi/example_load_gevi.py
@ -0,0 +1,56 @@
+# %%
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+
+output_path = 'output'
+
+recording_name = 'M0134M_2024-12-04_SessionA'
+n_trials_per_experiment = [30, 0, 30, 30, 30, 30, 30, 30, 30,]
+name_experiment = ['none', 'visual', '2 uA', '5 uA', '7 uA', '10 uA', '15 uA', '30 uA', '60 uA']
+
+#   recording_name = 'M0134M_2024-11-06_SessionB'
+#   n_trials_per_experiment = [15, 15,]
+#   name_experiment = ['none', 'visual',]
+
+i_experiment = 8
+
+r_avg = None
+ad_avg = None
+for i_trial in range(n_trials_per_experiment[i_experiment]):
+
+    folder = output_path + os.sep + recording_name 
+    file = f"Exp{i_experiment + 1:03}_Trial{i_trial + 1:03}_ratio_sequence.npz"
+    fullpath = folder + os.sep + file
+
+    print(f'Loading file "{fullpath}"...')
+    data = np.load(fullpath)
+
+    print(f"FIle contents: {data.files}")
+    ratio_sequence = data["ratio_sequence"]
+    if 'data_acceptor' in data.files:
+        data_acceptor = data["data_acceptor"]
+        data_donor = data["data_donor"]
+
+    mask = data["mask"][:, :, np.newaxis]
+
+    if i_trial == 0:
+        r_avg = ratio_sequence
+        if 'data_acceptor' in data.files:
+            ad_avg = (data_acceptor / data_donor) * mask + 1 - mask
+    else:
+        r_avg += ratio_sequence
+        if 'data_acceptor' in data.files:
+            ad_avg += (data_acceptor / data_donor) * mask + 1 - mask
+
+if r_avg is not None:
+    r_avg /= n_trials_per_experiment[i_experiment]
+if ad_avg is not None:
+    ad_avg /= n_trials_per_experiment[i_experiment]
+
+# %%
+for t in range(200, 300, 5):
+    plt.imshow(r_avg[:, :, t], vmin=0.99, vmax=1.01, cmap='seismic')
+    plt.colorbar()
+    plt.show()
+
--- a/other/stage_4b_inspect.py
+++ b/other/stage_4b_inspect.py
--- a/other/stage_4c_viewer.py
+++ b/other/stage_4c_viewer.py
--- a/preprocessing.pdf
+++ b/preprocessing.pdf
--- a/stage_5_convert_metadata.py
+++ b/stage_5_convert_metadata.py
@ -6,15 +6,13 @@ from functions.get_trials import get_trials
 from functions.get_experiments import get_experiments


-def converter(config_filename: str = "config.json") -> None:
+def converter(config_filename: str = "config_M_Sert_Cre_49.json") -> None:

-    filename: str = config_filename
-
-    if os.path.isfile(filename) is False:
-        print(f"{filename} is missing")
+    if os.path.isfile(config_filename) is False:
+        print(f"{config_filename} is missing")
        exit()

-    with open(filename, "r") as file:
+    with open(config_filename, "r") as file:
        config = json.loads(jsmin(file.read()))

    raw_data_path: str = os.path.join(
@ -30,6 +28,8 @@ def converter(config_filename: str = "config.json") -> None:

    experiments = get_experiments(raw_data_path).numpy()

+    os.makedirs(config["export_path"], exist_ok=True)
+
    for experiment in experiments:

        trials = get_trials(raw_data_path, experiment).numpy()
@ -44,7 +44,10 @@ def converter(config_filename: str = "config.json") -> None:
        ) as file:
            metadata = json.loads(jsmin(file.read()))

-        filename_out: str = f"meta_{config["mouse_identifier"]}_exp{experiment:03d}.json"
+        filename_out: str = os.path.join(
+            config["export_path"],
+            f"metadata_exp{experiment:03d}.json",
+        )

        with open(filename_out, 'w') as file:
            json.dump(metadata, file)
Author	SHA1	Message	Date
David Rotermund	6609a37a97	Add files via upload	2025-03-19 18:36:14 +01:00
David Rotermund	6d8a7fbbbc	Update stage_5_convert_metadata.py	2025-03-19 18:35:14 +01:00
David Rotermund	a33172f38b	Update README.md	2025-03-19 18:34:08 +01:00
David Rotermund	d0b8ff58d2	Add files via upload	2025-03-19 18:32:36 +01:00
David Rotermund	1946ecc343	Delete README.md	2025-03-19 18:32:03 +01:00
David Rotermund	d798311b0d	Delete stage_4_process.py	2025-03-19 18:29:54 +01:00
David Rotermund	2e36e9013c	Delete stage_4b_inspect.py	2025-03-19 18:29:46 +01:00
David Rotermund	c1caff162d	Delete stage_4c_viewer.py	2025-03-19 18:29:39 +01:00
David Rotermund	a3fe0e9d5f	Delete stage_3_refine_mask.py	2025-03-19 18:29:29 +01:00
David Rotermund	580a85b964	Delete stage_2_make_heartbeat_mask.py	2025-03-19 18:29:19 +01:00
David Rotermund	2d1772b948	Delete stage_1_get_ref_image.py	2025-03-19 18:29:09 +01:00
David Rotermund	389251826d	Delete stage_5_convert_metadata.py	2025-03-19 18:29:01 +01:00
David Rotermund	d8688a156a	Delete stage_6_convert_roi.py	2025-03-19 18:28:54 +01:00
David Rotermund	d3d79c0607	Delete geci_plot.py	2025-03-19 18:28:46 +01:00
David Rotermund	1b12b32a7d	Delete geci_loader.py	2025-03-19 18:28:39 +01:00
David Rotermund	943a0a09a0	Delete config_fatma_gevi_M0134M_SessionA2_Test.json	2025-03-19 18:28:29 +01:00
David Rotermund	c8b9fadade	Delete config_M_Sert_Cre_49.json	2025-03-19 18:28:19 +01:00
David Rotermund	0bb8964e1c	Delete config_M_Sert_Cre_46.json	2025-03-19 18:28:06 +01:00
David Rotermund	1902722901	Delete config_M_Sert_Cre_45.json	2025-03-19 18:27:57 +01:00
David Rotermund	2e1906fd64	Delete config_M_Sert_Cre_42.json	2025-03-19 18:27:49 +01:00
David Rotermund	f7f286689e	Delete config_M_Sert_Cre_41.json	2025-03-19 18:27:41 +01:00
David Rotermund	34eb1044d0	Delete config_M3879M_2021-10-05.json	2025-03-19 18:27:33 +01:00
David Rotermund	cfe688b0a3	Delete callum_config_M3905F.json	2025-03-19 18:27:19 +01:00
David Rotermund	a32fd9be39	Delete callum_config_M0134M.json	2025-03-19 18:27:10 +01:00
David Rotermund	859a945ac4	Delete functions directory	2025-03-19 18:26:40 +01:00