Update for higher density plate formats

README.md

@@ -1,18 +1,19 @@
-# Multi-Well Tools #
+# Nautilus Analysis #
 ## Tools to extract data produced by multi-well microscope experiments i.e. Nautilus ##
 
 ### Run the script from the command line ###
-` > python /path/to/well_data.py /path/to/json_config --input_video_path /path/to/input/video --output_dir_path /path/to/output/dir`</br></br>
+` > python /path/to/well_data.py /path/to/toml_config --input_video_path /path/to/input/video --output_dir_path /path/to/output/dir`</br></br>
 args with a leading -- are optional and if supplied will override keys with the same name in the json config.
 
 ### Basic System Test ###
-To run a basic system test, if you are in the main directory (multiwell_tools) :</br></br>
+To run a basic system test, if you are in the main directory (nautilus_analysis) :</br></br>
 
-python ./src/well_data.py "./test_data/CuriBio 24 Well Plate.json" --input_video_path .\test_data\default__2023_04_21_231442.raw --output_dir_path .\test_data\default__2023_04_21_231442Results --num_horizontal_pixels 1536 --num_vertical_pixels 1024 --num_frames 20 --bit_depth 16 --scale_factor 2 --duration 1 --fps 20
+python src\well_data.py test_data\settings.toml
 
 This will run the well data extraction function which will produce:
 * xlsx files with the time series data from each well,
 * a zip archive of all the xlsx files,
 * an image with the roi's drawn on one frame of the input video,
 * a plot of every wells time series data.
+* a csv file with the time series data from all wells