README.md

@@ -110,16 +110,31 @@ options:
      This algorithm is using [streak-finder package](https://github.com/simply-nicky/streak_finder) - a connection-based streak finding algorithm for convergent beam diffraction patterns.
 
      Input parameters:
+       * `'do_snr': 1/0` - Specifies whether to do whitefield and std correction, if selected - changes image and mask in place.
+       * `'std_data_file': str` - hdf5 data file containing pre-calculated std.
+       * `'std_dataset': str` - [optional] dataset containing pre-calculated std, defaults to `'entry/crystallography/std'`.
+       * `'whitefield_data_file': str` - hdf5 data file containing pre-calculated white field.
+       * `'whitefield_dataset': str` - [optional] dataset containing pre-calculated white field, defaults to `'entry/crystallography/whitefield'`.
+       * `'mask_data_file': str` - hdf5 data file containing pre-calculated mask.
+       * `'mask_dataset': str` - [optional] dataset containing pre-calculated mask, defaults to `'entry/instrument/detector/mask'`.
+       * `'scale_whitefield': 1/0` - Specifies whether to scale whitefield to signal, useful if intensity jumps.
+     
        * `'do_streakfinder_analysis': 1/0` - Specifies whether to execute the streak-finder algorithm.
-       * `'sf_structure_radius': int` - Connectivity structure radius.
-       * `'sf_structure_rank': int` - Connectivity structure rank.
-       * `'sf_min_size': float` - Minimum number of linelets required in a detected streak.
-       * `'sf_vmin': float` - Peak threshold. All peaks with values lower than ``sf_vmin`` are discarded.
+       * `'sf_peak_structure_radius': int` - Connectivity structure radius for *peaks* detection.
+       * `'sf_peak_structure_rank': int` - Connectivity structure rank for *peaks* detection.       
+       * `'sf_peak_vmin': float` - Peak threshold. All peaks with values lower than ``sf_peak_vmin`` are discarded.
        * `'sf_npts': int` - Support size threshold. The support structure is a connected set of pixels which
-                value is above the threshold ``sf_vmin``. A peak is discarded is the size of support
+                value is above the threshold ``sf_peak_vmin``. A peak is discarded is the size of support
                 set is lower than ``sf_npts``.
+       * `'sf_streak_structure_radius': int` - Connectivity structure radius for *streaks* detection.
+       * `'sf_streak_structure_rank': int` - Connectivity structure rank for *streaks* detection.       
+       * `'sf_streak_vmin': float` - Streak threshold. All streaks with values lower than ``sf_vmin`` are discarded.
+       * `'sf_min_size': float` - Minimum number of linelets required in a detected streak.
        * `'sf_xtol': float` - Distance threshold. A new linelet is added to a streak if it's distance to the
                 streak is no more than ``sf_xtol``.
+       * `'sf_nfa': 1` - Number of false alarms, allowed number of unaligned points in a streak.
+       * `'sf_num_threads': int` - Number of threads to use for peak finder algorithm
+       * `'sf_mask_rois': list[(int, int, int, int)]` - [optional] list of `(y_min, y_max, x_min, x_max)` coordinates of ROIs to mask out during peak finding; can be used to mask out bad regions as well as to reduce data size to e.g. one quadrant for the purpose of speedup. 
 
      Algorithm Output:
        * `'number_of_streaks': int` - Indicates the count of identified streaks.
@@ -258,22 +273,56 @@ Algorithms use input parameters specified in a JSON file provided to worker.py (
     "roi_y1": [],
     "roi_x2": [],
     "roi_y2": [], 
-    "do_whitefield_correction": 1,
-    "wf_data_file": "/sf/bernina/exp/00m_musterman/res/whitefield/JF07T32V01_wf_div.h5",
-    "wf_method": "div",
-    "apply_additional_mask_from_file": 1,
-    "mask_file": "/sf/bernina/exp/00m_musterman/res/mask/JF07T32V01_mask.h5", 
-    "do_streakfinder_analysis": 1,
-    "sf_structure_radius": 10,
-    "sf_structure_rank": 2,
-    "sf_min_size": 7,
-    "sf_vmin": 75,
-    "sf_npts":  100,
-    "sf_xtol": 1.5
-
 }
  ```
 
+Example JSON for Convergent-Beam Diffraction Streak-Finder:
+ ```json
+ {
+    "beam_center_x": 1119.0,
+    "beam_center_y": 1068.0,
+    "detector_distance": 0.092,
+    "do_peakfinder_analysis": 0,
+    "beam_energy": 11993.610318642704,
+    "apply_threshold": 0,
+    "threshold_min": 0,
+    "threshold_max": 35,
+    "apply_aggregation": 0,
+    "aggregation_max": 2,
+    "double_pixels": "mask",
+    "detector_rate": 100,
+    "do_radial_integration": 0,
+    "do_spi_analysis": 0,
+    "threshold_value": "NaN",
+    "select_only_ppicker_events": 0,
+    "disabled_modules": [],
+    "roi_x1": [],
+    "roi_y1": [],
+    "roi_x2": [],
+    "roi_y2": [],
+    "do_snr": 0,
+    "std_data_file": "/sf/instrument/exp/00m_mustermann/res/aux_data/streakfinder_metadata.h5",
+    "std_dataset": "entry/crystallography/std", 
+    "whitefield_data_file": "/sf/bernina/exp/00m_mustermann/res/aux_data/streakfinder_metadata.h5",
+    "whitefield_dataset": "entry/crystallography/whitefield", 
+    "mask_data_file": "/sf/bernina/exp/00m_mustermann/res/aux_data/JF_mask.h5",
+    "mask_dataset": "mask_data", 
+    "scale_whitefield": 0,
+    "do_streakfinder_analysis": 1,
+    "sf_peak_structure_radius": 2,
+    "sf_peak_structure_rank": 2,
+    "sf_peak_vmin": 50,
+    "sf_npts":  10,
+    "sf_streak_structure_radius": 6,
+    "sf_streak_structure_rank": 4,
+    "sf_xtol": 2.0,
+    "sf_streak_vmin": 30,
+    "sf_min_size": 25,
+    "sf_nfa": 1,
+    "sf_num_threads": 32,
+    "sf_mask_rois": [[0, 2216, 2107, 4215]]     
+}
+ ```
 # Acknowledgment
 
 Special thanks to Valerio Mariani for providing the cython implementation of peakfinder8.