implement frames_pattern, for custom removal of frames

bcdi/experiment/diffractometer.py

@@ -862,6 +862,7 @@ def load_check_dataset(
         scan_number,
         detector,
         setup,
+        frames_pattern=None,
         flatfield=None,
         hotpixels=None,
         background=None,
@@ -876,6 +877,9 @@ def load_check_dataset(
         :param scan_number: the scan number to load
         :param detector: an instance of the class Detector
         :param setup: an instance of the class Setup
+        :param frames_pattern: 1D array of int, of length data.shape[0]. If
+         frames_pattern is 0 at index, the frame at data[index] will be skipped,
+         if 1 the frame will added to the stack.
         :param flatfield: the 2D flatfield array
         :param hotpixels: the 2D hotpixels array. 1 for a hotpixel, 0 for normal pixels.
         :param background: the 2D background array to subtract to the data
@@ -947,7 +951,9 @@ def load_check_dataset(
             #################
             # select frames #
             #################
-            data, frames_logical = self.select_frames(data)
+            data, frames_logical = self.select_frames(
+                data=data, frames_pattern=frames_pattern
+            )
 
             #################################
             # crop the monitor if necessary #
@@ -1214,7 +1220,6 @@ def select_frames(data, frames_pattern=None):
            accordingly.
 
         """
-        # TODO implement this
         if frames_pattern is None:
             frames_pattern = np.ones(data.shape[0], dtype=int)
         valid.valid_1d_array(

bcdi/preprocessing/bcdi_utils.py

@@ -1265,8 +1265,11 @@ def load_bcdi_data(
      return a monitor based on the integrated intensity in the region of interest
      defined by detector.sum_roi, 'skip' to do nothing
     :param debugging:  set to True to see plots
-    :parama kwargs:
-     - 'photon_threshold' = float, photon threshold to apply before binning
+    :param kwargs:
+     - 'photon_threshold': float, photon threshold to apply before binning
+     - 'frames_pattern': 1D array of int, of length data.shape[0]. If
+       frames_pattern is 0 at index, the frame at data[index] will be skipped,
+       if 1 the frame will added to the stack.
 
     :return:
      - the 3D data and mask arrays
@@ -1279,7 +1282,7 @@ def load_bcdi_data(
     # check and load kwargs
     valid.valid_kwargs(
         kwargs=kwargs,
-        allowed_kwargs={"photon_threshold"},
+        allowed_kwargs={"photon_threshold", "frames_pattern"},
         name="kwargs",
     )
     photon_threshold = kwargs.get("photon_threshold", 0)
@@ -1289,12 +1292,20 @@ def load_bcdi_data(
         min_included=0,
         name="photon_threshold",
     )
+    frames_pattern = kwargs.get("frames_pattern")
+    valid.valid_1d_array(
+        frames_pattern,
+        allow_none=True,
+        allowed_values={0, 1},
+        name="frames_pattern"
+    )
 
     rawdata, rawmask, monitor, frames_logical = setup.diffractometer.load_check_dataset(
         logfile=logfile,
         scan_number=scan_number,
         detector=detector,
         setup=setup,
+        frames_pattern=frames_pattern,
         bin_during_loading=bin_during_loading,
         flatfield=flatfield,
         hotpixels=hotpixels,

bcdi/preprocessing/cdi_utils.py

@@ -615,7 +615,10 @@ def load_cdi_data(
      defined by detector.sum_roi
     :param debugging:  set to True to see plots
     :param kwargs:
-     - 'photon_threshold' = float, photon threshold to apply before binning
+     - 'photon_threshold': float, photon threshold to apply before binning
+     - 'frames_pattern': 1D array of int, of length data.shape[0]. If
+       frames_pattern is 0 at index, the frame at data[index] will be skipped,
+       if 1 the frame will added to the stack.
 
     :return:
      - the 3D data and mask arrays
@@ -629,7 +632,7 @@ def load_cdi_data(
     # check and load kwargs
     valid.valid_kwargs(
         kwargs=kwargs,
-        allowed_kwargs={"photon_threshold"},
+        allowed_kwargs={"photon_threshold", "frames_pattern"},
         name="kwargs",
     )
     photon_threshold = kwargs.get("photon_threshold", 0)
@@ -639,12 +642,20 @@ def load_cdi_data(
         min_included=0,
         name="photon_threshold",
     )
+    frames_pattern = kwargs.get("frames_pattern")
+    valid.valid_1d_array(
+        frames_pattern,
+        allow_none=True,
+        allowed_values={0, 1},
+        name="frames_pattern"
+    )
 
     rawdata, rawmask, monitor, frames_logical = setup.diffractometer.load_check_dataset(
         logfile=logfile,
         scan_number=scan_number,
         detector=detector,
         setup=setup,
+        frames_pattern=frames_pattern,
         bin_during_loading=bin_during_loading,
         flatfield=flatfield,
         hotpixels=hotpixels,

scripts/preprocessing/bcdi_preprocess_BCDI.py

@@ -72,6 +72,10 @@
 binning = (1, 2, 2)  # binning to apply to the data
 # (stacking dimension, detector vertical axis, detector horizontal axis)
 bin_during_loading = False  # True to bin during loading, require less memory
+frames_pattern = None
+# 1D array of int, of length data.shape[0]. If frames_pattern is 0 at index,
+# the frame at data[index] will be skipped, if 1 the frame will added to the stack.
+# Use this if you need to remove some frames and you know it in advance.
 ##############################
 # parameters used in masking #
 ##############################
@@ -768,6 +772,7 @@ def press_key(event):
             scan_number=scan_nb,
             detector=detector,
             setup=setup,
+            frames_pattern=frames_pattern,
             bin_during_loading=bin_during_loading,
             flatfield=flatfield,
             hotpixels=hotpix_array,

scripts/preprocessing/bcdi_preprocess_CDI.py

@@ -54,6 +54,10 @@
 binning = [1, 2, 2]  # binning that will be used for phasing
 # (stacking dimension, detector vertical axis, detector horizontal axis)
 bin_during_loading = False  # True to bin during loading, require less memory
+frames_pattern = None
+# 1D array of int, of length data.shape[0]. If frames_pattern is 0 at index,
+# the frame at data[index] will be skipped, if 1 the frame will added to the stack.
+# Use this if you need to remove some frames and you know it in advance.
 ##############################
 # parameters used in masking #
 ##############################
@@ -580,6 +584,7 @@ def press_key(event):
             scan_number=scan_nb,
             detector=detector,
             setup=setup,
+            frames_pattern=frames_pattern,
             bin_during_loading=bin_during_loading,
             flatfield=flatfield,
             hotpixels=hotpix_array,