Merge branch 'improve_invalid_frame' into 'master'

[patch-nx] add an option to convert automatically all frame of a given type...

Closes #82

See merge request !84

doc/tutorials/patch_nx.rst

@@ -66,6 +66,8 @@ Those are some examples of usage:
 
     # force frames 26 and 27 to be dark
     nxtomomill patch-nx --update-to-dark 26:28 simple_case.h5 entry
+    # force all projections to be dark
+    nxtomomill patch-nx --update-to-dark projection simple_case.h5 entry
     # force frames 10, 13, 16 and 19 to be flatfield
     nxtomomill patch-nx --update-to-flat 10:20:3 simple_case.h5 entry
     # force frame 0, 1 and to 4 to be projections
@@ -74,6 +76,8 @@ Those are some examples of usage:
     nxtomomill patch-nx --update-to-alignment 0 simple_case.h5 entry
     # force all frames to be invalid
     nxtomomill patch-nx --invalid-frames : simple_case.h5 entry
+    # force all "projection" frame to be invalid
+    nxtomomill patch-nx --invalid-frames projection simple_case.h5 entry
 
 
 .. note:: If you try to modify several frame type at the same type you should know that the order of resolution is:

nxtomomill/app/patch_nx.py

@@ -73,6 +73,8 @@ __date__ = "12/10/2020"
 import logging
 from nxtomomill import utils
 from silx.io.url import DataUrl
+from silx.utils.enum import Enum as _Enum
+from tomoscan.esrf.hdf5scan import HDF5TomoScan
 from nxtomomill.utils import ImageKey
 import argparse
 import os
@@ -92,10 +94,36 @@ _INFO_URL = (
     "of just by giving dataset_path@file_path".format(_SILX_DATA_URL)
 )
 
+
+class _ImageKeyName(_Enum):
+    ALIGNMENT = "alignment"
+    PROJECTION = "projection"
+    FLAT_FIELD = "flat"
+    DARK_FIELD = "dark"
+    INVALID = "invalid"
+
+    @staticmethod
+    def to_image_key(image_key) -> ImageKey:
+        image_key = _ImageKeyName.from_value(image_key.lower())
+        if image_key is _ImageKeyName.ALIGNMENT:
+            return ImageKey.ALIGNMENT
+        elif image_key is _ImageKeyName.PROJECTION:
+            return ImageKey.PROJECTION
+        elif image_key is _ImageKeyName.DARK_FIELD:
+            return ImageKey.DARK_FIELD
+        elif image_key is _ImageKeyName.FLAT_FIELD:
+            return ImageKey.FLAT_FIELD
+        elif image_key is _ImageKeyName.INVALID:
+            return ImageKey.INVALID
+        else:
+            raise ValueError(f"{image_key} not handled")
+
+
 _INFO_FRAME_INPUT = (
-    "Frames can be provided two ways: \n"
+    "Frames can be provided three ways: \n"
     "- has a list: frame_index_1,frame_index_2\n"
     "- has a python slice: from:to:steps\n"
+    f"- has an image key value. Valid values are {_ImageKeyName.values()}\n"
 )
 
 
@@ -131,7 +159,7 @@ def _extract_data_url(url_as_a_str):
             return url
 
 
-def _get_slice_to_modify(slice_as_str):
+def _get_slice_to_modify(slice_as_str, master_file, entry):
     """
     Return a list of int or a `slice` from  slice_as_str
     :param slice_as_str:
@@ -140,6 +168,15 @@ def _get_slice_to_modify(slice_as_str):
     """
     if slice_as_str is None:
         return None
+    elif slice_as_str.lower() in _ImageKeyName.values():
+        image_key = _ImageKeyName.to_image_key(slice_as_str)
+        scan = HDF5TomoScan(master_file, entry)
+        frames = scan.frames
+        slices = []
+        for frame in frames:
+            if frame.image_key is image_key:
+                slices.append(frame.index)
+        return slices
     elif ":" in slice_as_str:
         elmts = slice_as_str.split(":")
 
@@ -204,7 +241,7 @@ def main(argv):
     parser.add_argument(
         "--invalid-frames",
         default=None,
-        help="Define the set of frames to be mark as invalid. " "" + _INFO_FRAME_INPUT,
+        help="Define the set of frames to be mark as invalid. " + _INFO_FRAME_INPUT,
     )
     parser.add_argument(
         "--update-to-projection",
@@ -216,12 +253,12 @@ def main(argv):
     parser.add_argument(
         "--update-to-dark",
         default=None,
-        help="Define the set of frames to be mark as dark. " "" + _INFO_FRAME_INPUT,
+        help="Define the set of frames to be mark as dark. " + _INFO_FRAME_INPUT,
     )
     parser.add_argument(
         "--update-to-flat",
         default=None,
-        help="Define the set of frames to be mark as flat. " "" + _INFO_FRAME_INPUT,
+        help="Define the set of frames to be mark as flat. " + _INFO_FRAME_INPUT,
     )
     parser.add_argument(
         "--update-to-alignment",
@@ -247,11 +284,21 @@ def main(argv):
     patch_det_data = darks_start_url or flat_start_url or flat_end_url or darks_end_url
 
     # get information for modifying image_key
-    slice_to_update_to_dark = _get_slice_to_modify(options.update_to_dark)
-    slice_to_update_to_flat = _get_slice_to_modify(options.update_to_flat)
-    slice_to_update_to_projection = _get_slice_to_modify(options.update_to_projection)
-    slice_to_update_to_alignment = _get_slice_to_modify(options.update_to_alignment)
-    slice_to_invalid = _get_slice_to_modify(options.invalid_frames)
+    slice_to_update_to_dark = _get_slice_to_modify(
+        options.update_to_dark, master_file=options.file_path, entry=options.entry
+    )
+    slice_to_update_to_flat = _get_slice_to_modify(
+        options.update_to_flat, master_file=options.file_path, entry=options.entry
+    )
+    slice_to_update_to_projection = _get_slice_to_modify(
+        options.update_to_projection, master_file=options.file_path, entry=options.entry
+    )
+    slice_to_update_to_alignment = _get_slice_to_modify(
+        options.update_to_alignment, master_file=options.file_path, entry=options.entry
+    )
+    slice_to_invalid = _get_slice_to_modify(
+        options.invalid_frames, master_file=options.file_path, entry=options.entry
+    )
     patch_image_key = (
         slice_to_update_to_dark
         or slice_to_update_to_flat

nxtomomill/utils.py

@@ -55,18 +55,7 @@ import uuid
 from silx.io.utils import h5py_read_dataset
 import h5py._hl.selections as selection
 from h5py import h5s as h5py_h5s
-
-
-class ImageKey(_Enum):
-    """
-    Possible values of image_key_control
-    """
-
-    ALIGNMENT = -1
-    PROJECTION = 0
-    FLAT_FIELD = 1
-    DARK_FIELD = 2
-    INVALID = 3
+from tomoscan.esrf.hdf5scan import ImageKey
 
 
 class FieldOfView(_Enum):