Add temp directory for tests

MANIFEST.in

@@ -8,6 +8,10 @@ exclude *.ipynb
 
 recursive-include brainglobe_stitch *.py
 recursive-include brainglobe_stitch *.ijm
+recursive-include temp_directory *.h5
+recursive-include temp_directory *.txt
+recursive-include temp_directory *.xml
+
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

brainglobe_stitch/file_utils.py

@@ -28,7 +28,7 @@ def create_pyramid_bdv_h5(
     ----------
     input_file: Path
         The path to the input HDF5 file.
-    yield_progress:
+    yield_progress: bool, optional
         Whether to yield progress.
     """
     resolutions_array = np.array(

temp_directory/test_data_bdv.h5_meta.txt

@@ -0,0 +1,328 @@
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 561 nm
+[Intensity (%)] 20
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Right
+
+[POSITION]
+[x_pos] 29339.43
+[y_pos] 88449.64
+[f_start] 48850.0
+[f_end] 48850.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.632
+[etl_l_amplitude] 0.54
+[etl_r_offset] 1.42
+[etl_r_amplitude] 0.502
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 647 nm
+[Intensity (%)] 35
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Right
+
+[POSITION]
+[x_pos] 29339.43
+[y_pos] 88449.64
+[f_start] 48900.0
+[f_end] 48900.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.6239999999999999
+[etl_l_amplitude] 0.524
+[etl_r_offset] 1.445
+[etl_r_amplitude] 0.5
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 561 nm
+[Intensity (%)] 20
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Right
+
+[POSITION]
+[x_pos] 29339.43
+[y_pos] 87980.44
+[f_start] 48850.0
+[f_end] 48850.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.632
+[etl_l_amplitude] 0.54
+[etl_r_offset] 1.42
+[etl_r_amplitude] 0.502
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 647 nm
+[Intensity (%)] 35
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Right
+
+[POSITION]
+[x_pos] 29339.43
+[y_pos] 87980.44
+[f_start] 48900.0
+[f_end] 48900.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.6239999999999999
+[etl_l_amplitude] 0.524
+[etl_r_offset] 1.445
+[etl_r_amplitude] 0.5
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 561 nm
+[Intensity (%)] 20
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Left
+
+[POSITION]
+[x_pos] 28870.23
+[y_pos] 88449.64
+[f_start] 48850.0
+[f_end] 48850.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.632
+[etl_l_amplitude] 0.54
+[etl_r_offset] 1.42
+[etl_r_amplitude] 0.502
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 647 nm
+[Intensity (%)] 35
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Left
+
+[POSITION]
+[x_pos] 28870.23
+[y_pos] 88449.64
+[f_start] 48900.0
+[f_end] 48900.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.6239999999999999
+[etl_l_amplitude] 0.524
+[etl_r_offset] 1.445
+[etl_r_amplitude] 0.5
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 561 nm
+[Intensity (%)] 20
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Left
+
+[POSITION]
+[x_pos] 28870.23
+[y_pos] 87980.44
+[f_start] 48850.0
+[f_end] 48850.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.632
+[etl_l_amplitude] 0.54
+[etl_r_offset] 1.42
+[etl_r_amplitude] 0.502
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128
+[Metadata for file] E:/User/test_data_bdv.h5
+
+[CFG]
+[Laser] 647 nm
+[Intensity (%)] 35
+[Zoom] 1.6x
+[Pixelsize in um] 4.08
+[Filter] 405-488-561-640-Quadrupleblock
+[Shutter] Left
+
+[POSITION]
+[x_pos] 28870.23
+[y_pos] 87980.44
+[f_start] 48900.0
+[f_end] 48900.0
+[z_start] -550.02
+[z_end] 0.0
+[z_stepsize] 5.0
+[z_planes] 110
+[rot] 177.20002
+
+[ETL PARAMETERS]
+[ETL CFG File] C:/MesoSPIM/Control/mesoSPIM/config/etl_parameters/ETL-parameters_SWC.csv
+[etl_l_offset] 1.6239999999999999
+[etl_l_amplitude] 0.524
+[etl_r_offset] 1.445
+[etl_r_amplitude] 0.5
+
+[GALVO PARAMETERS]
+[galvo_l_frequency] 199.9
+[galvo_l_amplitude] 5.0
+[galvo_l_offset] -0.12
+[galvo_r_amplitude] 5.0
+[galvo_r_offset] 0.0
+
+[CAMERA PARAMETERS]
+[camera_type] HamamatsuOrca
+[camera_exposure] 0.015
+[camera_line_interval] 7.5e-05
+[x_pixels] 128
+[y_pixels] 128