Replace text file with iterable

Ignored projections will be provided directly with an iterable rather than in a file to read

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
@@ -75,7 +75,7 @@ class EDFTomoScan(TomoScanBase):
         self,
         scan: Union[str, None],
         n_frames: Union[int, None] = None,
-        ignore_projections: Union[None, str] = None,
+        ignore_projections: Union[None, Iterable] = None,
     ):
         TomoScanBase.__init__(
             self, scan=scan, type_=self._TYPE, ignore_projections=ignore_projections
@@ -269,8 +269,8 @@ class EDFTomoScan(TomoScanBase):
             else:
                 self._projections = all_projections
                 self._alignment_projections = {}
-            if self._ignored_projections is not None:
-                for idx in self._ignored_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)

tomoscan/esrf/hdf5scan.py

@@ -118,7 +118,7 @@ class HDF5TomoScan(TomoScanBase):
         scan: str,
         entry: str = None,
         index: typing.Union[int, None] = 0,
-        ignore_projections: typing.Union[None, str] = None,
+        ignore_projections: typing.Union[None, typing.Iterable] = None,
     ):
         if entry is not None:
             index = None
@@ -336,8 +336,8 @@ class HDF5TomoScan(TomoScanBase):
         if self._projections is None:
             if self.frames:
                 ignored_projs = []
-                if self._ignored_projections is not None:
-                    ignored_projs = self._ignored_projections
+                if self.ignore_projections is not None:
+                    ignored_projs = self.ignore_projections
                 proj_frames = tuple(
                     filter(
                         lambda x: (

tomoscan/esrf/test/test_edfscan.py

@@ -607,13 +607,6 @@ class TestIgnoredProjections(unittest.TestCase):
     def setUp(self) -> None:
         self.folder = tempfile.mkdtemp()
         self.ignored_projs = [5, 6, 7]
-        self.ignored_projs_fname = os.path.join(self.folder, "ignored_projections.txt")
-        numpy.savetxt(
-            self.ignored_projs_fname,
-            self.ignored_projs,
-            header="Indices of ignored projections",
-            comments="#",
-        )
 
     def tearDown(self) -> None:
         shutil.rmtree(self.folder)
@@ -623,10 +616,7 @@ class TestIgnoredProjections(unittest.TestCase):
             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_fname
-        )
-        self.assertTrue(numpy.allclose(scan._ignored_projections, self.ignored_projs))
+        scan = EDFTomoScan(scan=self.folder, ignore_projections=self.ignored_projs)
         for idx in self.ignored_projs:
             self.assertFalse(
                 idx in scan.projections,

tomoscan/esrf/test/test_hdf5scan.py

@@ -318,24 +318,12 @@ class TestIgnoredProjections(HDF5TestBaseClass):
         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]
-        self.ignored_projs_fname = os.path.join(
-            self.test_dir, "ignored_projections.txt"
-        )
-        numpy.savetxt(
-            self.ignored_projs_fname,
-            self.ignored_projs,
-            header="Indices of ignored projections",
-            comments="#",
-        )
 
     def testIgnoreProjections(self):
         self.scan = HDF5TomoScan(
-            scan=self.dataset_file, ignore_projections=self.ignored_projs_fname
+            scan=self.dataset_file, ignore_projections=self.ignored_projs
         )
         self.scan._projections = None
-        self.assertTrue(
-            numpy.allclose(self.scan._ignored_projections, self.ignored_projs)
-        )
         for idx in self.ignored_projs:
             self.assertFalse(
                 idx in self.scan.projections,

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
@@ -74,7 +74,7 @@ class TomoScanBase:
         self,
         scan: Union[None, str],
         type_: str,
-        ignore_projections: Union[None, str] = None,
+        ignore_projections: Union[None, Iterable] = None,
     ):
         self.path = scan
         self._type = type_
@@ -92,7 +92,7 @@ class TomoScanBase:
         self._flats_weights = None
         """list flats indexes to use for flat field correction and associate
         weights"""
-        self._get_ignored_projections(ignore_projections)
+        self.ignore_projections = ignore_projections
 
     def clear_caches(self):
         """clear caches. Might be call if some data changed after
@@ -634,15 +634,3 @@ class TomoScanBase:
             for proj_index in self.projections:
                 res[proj_index] = get_weights(proj_index=proj_index)
             return res
-
-    def _get_ignored_projections(self, ignore_projections):
-        self.ignore_projections = ignore_projections
-        self._ignored_projections = None
-        if ignore_projections is not None:
-            self._ignored_projections = numpy.loadtxt(ignore_projections, comments="#")
-            if self._ignored_projections.ndim > 1:
-                raise ValueError(
-                    "Expected exactly one row or one column in file %s"
-                    % ignore_projections
-                )
-            self._ignored_projections = self._ignored_projections.astype(numpy.uint32)