IPTS-34718 data analysis
Create a working folder (this is where all the files will be created)
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type (replace your_folder_name by a name you chose yourself.
$ mkdir /HFIR/CG1D/IPTS-34718/shared/processed_data/<your_folder_name>
Normalize the data
You can either normalize them by OB or by the first image of the stack. Either way, use the notebook (https://neutronimaging.ornl.gov/tutorials/imaging-notebooks/normalization/manual-normalization/).
Make sure you select the first image instead of the OB when you want to divide by the first image.
From now on, we will work with the normalized images
Create file name vs time stamp ascii file
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To do so, we will use the imaging notebook called create_list_of_file_name_vs_time_stamp.ipynb (https://neutronimaging.ornl.gov/tutorials/imaging-notebooks/create-list-of-file-names-vs-time-stamp/)
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Follow the tutorial on each folder to create those files.
NB: My recommendation would be to create that ascii file into a folder located in /HFIR/CG1D/IPTS-34718/shared/processed_data/<your_folder_name>
Create an ascii file of mean counts of region of interest (ROI) for each image
For this, we will use ImageJ
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Load the entire stack of images and select the folder to process. Make sure you DO NOT CHECK ‘use virtual stack’. This will take up to a few minutes (depending on how many images are in the folder).
2. Let’s crop the images to only keep the region of interest
3. let’s select a ROI and get the Mean count of that region for each image and export the data into an ascii file
Display counts vs file index and vs time stamp
For the rest of the work, we will need to use the custom notebook I wrote for you. To launch that notebook, go to the analysis.sns.gov machine. Follow the instructions explained here and look at the GUI section. You will need to enter your IPTS number (34718). Select the notebook called data_analysis_from_mean_region_to_plots.ipynb.
NB: SAVE_AS this notebook in order to keep the original version untouched!
