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…dex for the darks (eg below the first 10 time bins use that as the dark spectrum)
…ization also IRF fitting that is dubious right now but fits something
merging master to the current experiment to capture the recent PR for the dark shot changes.
…rence_spectrum-should-have-a-feature-to-make-difference-based-on-indices 21 xspectvisualizationplot 2d difference spectrum should have a feature to make difference based on indices
…. Scaled fast_delay_key values by 1e12 in time_binning method in XSpect_Analysis.py. Created a current clean and working notebook XSpect_XES_dehe_on_demand_05022025.ipynb
…n_demand, etc. Renamed the notebooks so that they are unique and they don't conflict with merges from others. It would be good to come up with a system/protocol for git and notebook.
…heritance chain. It doesn't seem to break anything. I just think it is neater that way.
Merging code changes from Dehe for Follmer experiment
Mfx10089224
…eys are unique and not duplicates in the final set of attributed.
This commit introduces a new method, `primary_analysis_static_laser`, specifically designed for analyzing data with static laser conditions. This method now separates shots based on laser presence and applies hitfinding and spatial reduction steps individually to the resulting shot subsets: 'epix', 'epix_simultaneous_laser', and 'epix_xray_not_laser'. This allows for a more granular analysis of laser-related effects. Key changes: * Added `primary_analysis_static_laser` method for laser analysis. * Modified the laser analysis method to filter shots and handle hitfinding, transposition, patching, rotation and spatial reduction for different shot types to enable laser-specific filtering and analysis. * Updated `keys_to_save` to include results from laser-specific analysis.
…tra (i.e. no laser)
…his at the object level
…zation taking the absolute value of the trapz because the energy axis direction changes the values of the trapezoidal integrals.
…ector_temporal in analysis so that each pixel has an std calculated per time bin, then error is propagated at controller level when runs are summed and differences calculated.
Droplet analysis working
…e list for angles for rotation. The length of the list should match the length of ROIs given, in which case each ROI will be rotated by the matched indexed angle provided. Otherwise, if one angle (not list) is given, the one angle will be applied to all ROIs. Or if the length of angle list does not match length of ROI list, only the first angle will be accepted and applied to all ROIs.
Droplet analysis working, can apply multiple rotation angles to multiple ROIs
… use supplied values to calculate the energy axis, otherwise the energy axis remains in pixels. Also commented out some minor print statements in Analysis and Controller. Visualization also has changes but those things are likely broken after merge with Ryan's changes from the droplet feature branch.
…t some list of arbitrary pixel values and path them. New changes check if pixels_to_patch attribute exists and patches pixels if true.
…Reworked parallelization to add timeout for individual tasks, in case a single tasks hangs up. Rewrites timeout errors with run run_shot_batch to update status. Changed analyzed_runs list so that if the results are successful they are directly written to self.analyzed_runs instead of waiting for all results to finish. Added a few other update status messages to help monitor/debug. 2. Fixed diff_slice method in visualization to work with latest code changes.
… issue with the pull request where the conflict cannot easily be resovled. I think in general we should consider creating some guidelines for the notebook management bc they are plain text json with code and image data in them and git has a hard time handling them
…g analyzed runs into analysis method combine_runs. (2) Removed plot_2d_difference_spectrum extent option in plt.imshow that was throwing an error (bc the energy axis attribute names have changed). I don't think the extent is necessary. (3) Added vim swap (temp) files to .gitignore.
…es rotation cases. Angle list was supplied to %f and it was breaking the analsis.
…anch for current experiment: https://github.com/lg345/XSpect/tree/mfx101338925.
…sults optional parameter that returns the results of SVD analysis if set to true (3) tweak plot scaling/viz things
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Docs are out of date compared to master. Need to merge master changes into jtb to build docs.