Merge branch 'ignore_projections' into 'master'

Ignore projections

See merge request !29

tomoscan/esrf/edfscan.py

@@ -37,7 +37,7 @@ import copy
 from lxml import etree
 import json
 import io
-from typing import Union
+from typing import Union, Iterable
 from ..scanbase import TomoScanBase
 from .utils import get_parameters_frm_par_or_info, extract_urls_from_edf
 from ..unitsystem.metricsystem import MetricSystem
@@ -71,8 +71,15 @@ class EDFTomoScan(TomoScanBase):
 
     _SCHEME = "fabio"
 
-    def __init__(self, scan: Union[str, None], n_frames: Union[int, None] = None):
-        TomoScanBase.__init__(self, scan=scan, type_=self._TYPE)
+    def __init__(
+        self,
+        scan: Union[str, None],
+        n_frames: Union[int, None] = None,
+        ignore_projections: Union[None, Iterable] = None,
+    ):
+        TomoScanBase.__init__(
+            self, scan=scan, type_=self._TYPE, ignore_projections=ignore_projections
+        )
 
         # data caches
         self._darks = None
@@ -262,6 +269,9 @@ class EDFTomoScan(TomoScanBase):
             else:
                 self._projections = all_projections
                 self._alignment_projections = {}
+            if self.ignore_projections is not None:
+                for idx in self.ignore_projections:
+                    self._projections.pop(idx, None)
 
             self._darks = EDFTomoScan.get_darks_url(self.path)
             self._flats = EDFTomoScan.get_refs_url(self.path)

tomoscan/esrf/hdf5scan.py

@@ -113,7 +113,11 @@ class HDF5TomoScan(TomoScanBase):
     _EPSILON_ROT_ANGLE = 0.02
 
     def __init__(
-        self, scan: str, entry: str = None, index: typing.Union[int, None] = 0
+        self,
+        scan: str,
+        entry: str = None,
+        index: typing.Union[int, None] = 0,
+        ignore_projections: typing.Union[None, typing.Iterable] = None,
     ):
         if entry is not None:
             index = None
@@ -130,7 +134,9 @@ class HDF5TomoScan(TomoScanBase):
         else:
             self.master_file = None
 
-        super(HDF5TomoScan, self).__init__(scan=scan, type_=HDF5TomoScan._TYPE)
+        super(HDF5TomoScan, self).__init__(
+            scan=scan, type_=HDF5TomoScan._TYPE, ignore_projections=ignore_projections
+        )
 
         if scan is None:
             self._entry = None
@@ -328,10 +334,16 @@ class HDF5TomoScan(TomoScanBase):
     def projections(self) -> typing.Union[dict, None]:
         if self._projections is None:
             if self.frames:
+                ignored_projs = []
+                if self.ignore_projections is not None:
+                    ignored_projs = self.ignore_projections
                 proj_frames = tuple(
                     filter(
-                        lambda x: x.image_key == ImageKey.PROJECTION
-                        and x.is_control == False,
+                        lambda x: (
+                            x.image_key == ImageKey.PROJECTION
+                            and x.index not in ignored_projs
+                            and x.is_control == False
+                        ),
                         self.frames,
                     )
                 )

tomoscan/esrf/test/test_edfscan.py

@@ -601,6 +601,29 @@ class TestScanBaseJSON(unittest.TestCase):
                 scan_to_update.load_from_dict(outfile)
 
 
+class TestIgnoredProjections(unittest.TestCase):
+    """Test the ignore_projections parameter"""
+
+    def setUp(self) -> None:
+        self.folder = tempfile.mkdtemp()
+        self.ignored_projs = [5, 6, 7]
+
+    def tearDown(self) -> None:
+        shutil.rmtree(self.folder)
+
+    def testIgnoreProjections(self):
+        mock = MockEDF(
+            scan_path=self.folder, n_radio=15, n_ini_radio=10, n_extra_radio=0, dim=10
+        )
+        mock.end_acquisition()
+        scan = EDFTomoScan(scan=self.folder, ignore_projections=self.ignored_projs)
+        for idx in self.ignored_projs:
+            self.assertFalse(
+                idx in scan.projections,
+                "Projection index %d is supposed to be ignored" % idx,
+            )
+
+
 def suite():
     test_suite = unittest.TestSuite()
     for ui in (
@@ -613,6 +636,7 @@ def suite():
         TestOriDarksFlats,
         TestFlatFieldCorrection,
         TestGetSinogram,
+        TestIgnoredProjections,
     ):
         test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
     return test_suite

tomoscan/esrf/test/test_hdf5scan.py

@@ -34,7 +34,7 @@ import os
 import tempfile
 from tomoscan.test.utils import UtilsTest
 from tomoscan.esrf.hdf5scan import HDF5TomoScan, ImageKey, Frame
-from ...unitsystem import metricsystem
+from tomoscan.unitsystem import metricsystem
 from silx.io.utils import get_data
 import numpy
 
@@ -311,9 +311,34 @@ class TestGetSinogram(HDF5TestBaseClass):
             self.scan.get_sinogram(line=25, subsampling=1)
 
 
+class TestIgnoredProjections(HDF5TestBaseClass):
+    """Test the ignore_projections parameter"""
+
+    def setUp(self) -> None:
+        super(TestIgnoredProjections, self).setUp()
+        self.dataset_file = self.get_dataset("frm_edftomomill_oneentry.nx")
+        self.ignored_projs = [387, 388, 389, 390, 391, 392, 393, 394, 395, 396]
+
+    def testIgnoreProjections(self):
+        self.scan = HDF5TomoScan(
+            scan=self.dataset_file, ignore_projections=self.ignored_projs
+        )
+        self.scan._projections = None
+        for idx in self.ignored_projs:
+            self.assertFalse(
+                idx in self.scan.projections,
+                "Projection index %d is supposed to be ignored" % idx,
+            )
+
+
 def suite():
     test_suite = unittest.TestSuite()
-    for ui in (TestHDF5Scan, TestFlatFieldCorrection, TestGetSinogram):
+    for ui in (
+        TestHDF5Scan,
+        TestFlatFieldCorrection,
+        TestGetSinogram,
+        TestIgnoredProjections,
+    ):
         test_suite.addTest(unittest.defaultTestLoader.loadTestsFromTestCase(ui))
     return test_suite
 

tomoscan/scanbase.py

@@ -32,7 +32,7 @@ import os
 import typing
 import logging
 import numpy
-from typing import Union
+from typing import Union, Iterable
 from collections import OrderedDict
 from .unitsystem.metricsystem import MetricSystem
 from silx.utils.enum import Enum as _Enum
@@ -70,7 +70,12 @@ class TomoScanBase:
     _SCHEME = None
     """scheme to read data url for this type of acquisition"""
 
-    def __init__(self, scan: Union[None, str], type_: str):
+    def __init__(
+        self,
+        scan: Union[None, str],
+        type_: str,
+        ignore_projections: Union[None, Iterable] = None,
+    ):
         self.path = scan
         self._type = type_
         self._normed_flats = None
@@ -87,6 +92,7 @@ class TomoScanBase:
         self._flats_weights = None
         """list flats indexes to use for flat field correction and associate
         weights"""
+        self.ignore_projections = ignore_projections
 
     def clear_caches(self):
         """clear caches. Might be call if some data changed after