Correct setting name for mask form file dataset; prepend all strak-finder-specific settings names with sf; Make streak-finder mask optional now that we have mask from file

README.md

@@ -111,13 +111,13 @@ options:
 
      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.
+       * `'sf_std_data_file': str` - hdf5 data file containing pre-calculated std.
+       * `'sf_std_dataset': str` - [optional] dataset containing pre-calculated std, defaults to `'entry/crystallography/std'`.
+       * `'sf_whitefield_data_file': str` - hdf5 data file containing pre-calculated white field.
+       * `'sf_whitefield_dataset': str` - [optional] dataset containing pre-calculated white field, defaults to `'entry/crystallography/whitefield'`.
+       * `'sf_mask_data_file': str` - [optional] hdf5 data file containing pre-calculated mask.
+       * `'sf_mask_dataset': str` - [optional] dataset containing pre-calculated mask, defaults to `'entry/instrument/detector/mask'`.
+       * `'sf_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_peak_structure_radius': int` - Connectivity structure radius for *peaks* detection.
@@ -245,7 +245,7 @@ options:
       Input parameters:
        * `'apply_additional_mask': 1/0` - Input flag to enable this functionality.
        * `'mask_file': str` - Path to the hdf5 or npy file with mask data.
-       * `'mask_ds': str` [Optional] - Name of the dataset containing mask in the hdf5 file, default is `"mask_data"`.
+       * `'mask_dataset': str` [Optional] - Name of the dataset containing mask in the hdf5 file, default is `"mask_data"`.
       Algorithm Output:
         * `'mask_from_file_applied': 1/0` - Indicates whether the algorithm ran successfully.
      
@@ -314,14 +314,17 @@ Example JSON for Convergent-Beam Diffraction Streak-Finder:
     "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",
+    "": 1,
+    "mask_file": "/sf/jungfrau/config/additional_mask/JF07T32V02.h5",
     "mask_dataset": "mask_data", 
-    "scale_whitefield": 0,
+    "do_snr": 0,
+    "sf_std_data_file": "/sf/instrument/exp/00m_mustermann/res/aux_data/streakfinder_metadata.h5",
+    "sf_std_dataset": "entry/crystallography/std", 
+    "sf_whitefield_data_file": "/sf/bernina/exp/00m_mustermann/res/aux_data/streakfinder_metadata.h5",
+    "sf_whitefield_dataset": "entry/crystallography/whitefield", 
+    "sf_mask_data_file": "/sf/bernina/exp/00m_mustermann/res/aux_data/JF_mask.h5",
+    "sf_mask_dataset": "mask_data", 
+    "sf_scale_whitefield": 0,
     "do_streakfinder_analysis": 1,
     "sf_negative_handler": "zero", 
     "sf_peak_structure_radius": 2,

dap/algos/addmaskfile.py

@@ -13,7 +13,7 @@ def calc_apply_additional_mask_from_file(results, pixel_mask_pf):
     mask_file = results.get("mask_file", None)
     if not mask_file:
         return
-    mask_dataset = results.get("mask_ds", DEFAULT_MASK_DATASET)
+    mask_dataset = results.get("mask_dataset", DEFAULT_MASK_DATASET)
 
     # Support for hdf5 and npy
     if mask_file.endswith(".npy"):

dap/algos/streakfind.py

@@ -45,7 +45,6 @@ def calc_streakfinder_analysis(results, data, pf_pixel_mask):
     if do_snr:
         # Changes data and mask in-place
         data = cryst_data.snr[0].copy()
-        np.multiply(pf_pixel_mask, cryst_data.mask, out=pf_pixel_mask)
 
     try:
         _calc_streakfinder_analysis(results, cryst_data)
@@ -56,40 +55,43 @@ def calc_streakfinder_analysis(results, data, pf_pixel_mask):
 
 def _generate_cryst_data(results, data, pf_pixel_mask) -> CrystData:
     params_required = [
-        "whitefield_data_file",
-        "mask_data_file",
-        "std_data_file",
-        "scale_whitefield",  # Bool
+        "sf_whitefield_data_file",
+        "sf_std_data_file",
+        "sf_scale_whitefield",  # Bool
     ]
 
     if not all(param in results.keys() for param in params_required):
         raise ValueError(f"ERROR: Not enough parameters for CBD correction. Skipping\n"
               f"{params_required=}")
 
-    whitefield_data_file = results["whitefield_data_file"]
-    mask_data_file = results["mask_data_file"]
-    std_data_file = results["std_data_file"]
-    scale_whitefield = results["scale_whitefield"]
+    whitefield_data_file = results["sf_whitefield_data_file"]
+    std_data_file = results["sf_std_data_file"]
+    scale_whitefield = results["sf_scale_whitefield"]
 
     # Using CXI Store specification as default
-    whitefield_dataset = results.get("whitefield_dataset", "entry/crystallography/whitefield")
-    mask_dataset = results.get("mask_dataset", "entry/instrument/detector/mask")
-    std_dataset = results.get("std_dataset", "entry/crystallography/std")
+    whitefield_dataset = results.get("sf_whitefield_dataset", "entry/crystallography/whitefield")
+    std_dataset = results.get("sf_std_dataset", "entry/crystallography/std")
 
-    num_threads = results.get("num_threads", DEFAULT_NUM_THREADS)
+    num_threads = results.get("sf_num_threads", DEFAULT_NUM_THREADS)
 
     with h5py.File(whitefield_data_file, "r") as hf:
         whitefield = hf[whitefield_dataset][:]
 
-    with h5py.File(mask_data_file, "r") as hf:
-        mask = hf[mask_dataset][:].astype(np.bool)
-
     with h5py.File(std_data_file, "r") as hf:
         std = hf[std_dataset][:]
 
+    mask_data_file = results.get("sf_mask_data_file", None)
+    if mask_data_file is None:
+        mask = pf_pixel_mask
+    else:
+        mask_dataset = results.get("sf_mask_dataset", "entry/instrument/detector/mask")
+        with h5py.File(mask_data_file, "r") as hf:
+            mask = hf[mask_dataset][:].astype(np.bool)
+        mask *= pf_pixel_mask
+
     data = CrystData(
         data=data[np.newaxis, :],
-        mask=mask*pf_pixel_mask,
+        mask=mask,
         std=std,
         whitefield=whitefield
     )