tomwer 1.2.0a2__py3-none-any.whl → 1.2.0a4__py3-none-any.whl

tomwer/core/process/reconstruction/nabu/nabuvolume.py

@@ -224,7 +224,9 @@ class VolumeRunner(_NabuBaseReconstructor):
         # force overwrite results
         if "output" not in self.configuration:
             self.configuration["output"] = {}
-        config_slices = self._treateOutputConfig(self.configuration)
+        config_slices, cfg_folder = self._treateOutputConfig(self.configuration)
+
+        # force overwriting results
         config_slices["output"].update({"overwrite_results": 1})
 
         # check and clamp `start_z` and `end_z`
@@ -242,12 +244,6 @@ class VolumeRunner(_NabuBaseReconstructor):
                     value = -1
                 config_slices["reconstruction"][key] = value
 
-        cfg_folder = os.path.join(
-            config_slices["output"]["location"], settings.NABU_CFG_FILE_FOLDER
-        )
-        if not os.path.exists(cfg_folder):
-            os.makedirs(cfg_folder)
-
         name = (
             config_slices["output"]["file_prefix"] + settings.NABU_CONFIG_FILE_EXTENSION
         )
@@ -256,6 +252,9 @@ class VolumeRunner(_NabuBaseReconstructor):
         conf_file = os.path.join(cfg_folder, name)
         _logger.info(f"{self.scan}: create {conf_file}")
 
+        # make sure output location exists
+        os.makedirs(config_slices["output"]["location"], exist_ok=True)
+
         # add some tomwer metadata and save the configuration
         # note: for now the section is ignored by nabu but shouldn't stay that way
         with utils.TomwerInfo(config_slices) as config_to_dump:
@@ -317,7 +316,9 @@ class VolumeRunner(_NabuBaseReconstructor):
         :return: (nabu config dict, nabu extra options)
         """
         config = copy.deepcopy(config)
-        config = super()._treateOutputSliceConfig(config)
+        config, nabu_cfg_folder = super()._treateOutputSliceConfig(config)
+        os.makedirs(config["output"]["location"], exist_ok=True)
+
         # adapt config_s to specific volume treatment
         if "postproc" in config:
             config["postproc"] = config["postproc"]
@@ -329,7 +330,7 @@ class VolumeRunner(_NabuBaseReconstructor):
             config["reconstruction"]["end_z"] = config["end_z"]
             del config["end_z"]
 
-        return config
+        return config, nabu_cfg_folder
 
     @docstring(_NabuBaseReconstructor)
     def _get_file_basename_reconstruction(self, pag, db, ctf):

tomwer/core/process/reconstruction/nabu/utils.py

@@ -159,7 +159,7 @@ def get_recons_volume_identifier(
     if file_format in ("hdf5", "h5", "hdf"):
         if slice_index is not None:
             # case of a single hdf5 file
-            file_name = "_".join((file_prefix, str(slice_index).zfill(4)))
+            file_name = "_".join((file_prefix, str(slice_index).zfill(6)))
         else:
             file_name = file_prefix
         file_name = ".".join((file_name, file_format))
@@ -179,23 +179,13 @@ def get_recons_volume_identifier(
     elif file_format in ("vol", "raw"):
         if slice_index is not None:
             # case of a single hdf5 file
-            file_name = "_".join((file_prefix, str(slice_index).zfill(4)))
+            file_name = "_".join((file_prefix, str(slice_index).zfill(6)))
         else:
             file_name = file_prefix
-        # on 2022.3.x the location seems invalid for nabu. Add this second location to
-        # handle most of the case.
-        fix_nabu = os.path.join(file_prefix, file_name)
-
         file_name = ".".join((file_name, file_format))
         file_path = os.path.join(location, file_name)
 
-        file_name_fix_nabu = ".".join((fix_nabu, file_format))
-        file_path_fix_nabu = os.path.join(location, file_name_fix_nabu)
-
-        volumes = (
-            RawVolume(file_path=file_path_fix_nabu),
-            RawVolume(file_path=file_path),
-        )
+        volumes = (RawVolume(file_path=file_path),)
     elif file_format in ("jp2", "jp2k", "edf", "tiff"):
         if file_format in ("jp2k", "jp2"):
             constructor = JP2KVolume
@@ -205,31 +195,15 @@ def get_recons_volume_identifier(
             constructor = TIFFVolume
         else:
             raise NotImplementedError
-        output_extension = file_format
         basename = file_prefix
+        file_path = location
+        volumes = (
+            constructor(
+                folder=location,
+                volume_basename=basename,
+            ),
+        )
 
-        if slice_index is None and start_z is None and end_z is None:
-            # if this is a single slice
-            file_path = ".".join(
-                (
-                    os.path.join(location, file_prefix, file_prefix),
-                    output_extension,
-                )
-            )
-            # TODO: in the future we might want to provide data_slice according to z values
-            volumes = (
-                constructor(
-                    folder=os.path.join(location, file_prefix),
-                    volume_basename=basename,
-                ),
-            )
-        else:
-            volumes = (
-                constructor(
-                    folder=os.path.join(location, file_prefix),
-                    volume_basename=basename,
-                ),
-            )
     # case of the multitiff. Not handled by tomwer
     # elif file_format == "tiff":
     #     # for single frame tiff nabu uses another convention by saving it 'directly'.

tomwer/core/process/test/test_nabu.py

@@ -127,7 +127,7 @@ class TestNabuIni(unittest.TestCase):
         # check volume and slice .cfg files for nabu reconstruction are here
         for file_name in (
             os.path.basename(self.scan.path) + ".cfg",
-            os.path.basename(self.scan.path) + "slice_0001" + ".cfg",
+            os.path.basename(self.scan.path) + "slice_000001" + ".cfg",
         ):
             with self.subTest(file_name=file_name):
                 self.assertTrue(
@@ -151,7 +151,7 @@ class TestNabuIni(unittest.TestCase):
         # check volume and slice .cfg files for nabu reconstruction are here
         for file_name in (
             os.path.basename(self.scan.path) + "pag_db0100.cfg",
-            os.path.basename(self.scan.path) + "slice_pag_0001_db0100" + ".cfg",
+            os.path.basename(self.scan.path) + "slice_pag_000001_db0100" + ".cfg",
         ):
             with self.subTest(file_name=file_name):
                 self.assertTrue(
@@ -178,7 +178,7 @@ class TestNabuIni(unittest.TestCase):
             ini_files.append(
                 os.path.basename(self.scan.path)
                 + "slice_"
-                + str(slice_index).zfill(4)
+                + str(slice_index).zfill(6)
                 + ".cfg"
             )
 
@@ -222,7 +222,7 @@ class TestNabuIni(unittest.TestCase):
             # add slice ini file
             ini_files.append(
                 os.path.basename(self.scan.path)
-                + "slice_pag_0001_db"
+                + "slice_pag_000001_db"
                 + str(int(pag_db)).zfill(4)
                 + ".cfg"
             )
@@ -265,7 +265,7 @@ class TestNabuIni(unittest.TestCase):
                 ini_files.append(
                     os.path.basename(self.scan.path)
                     + "slice_pag_"
-                    + str(slice_index).zfill(4)
+                    + str(slice_index).zfill(6)
                     + "_db"
                     + str(pag_db).zfill(4)
                     + ".cfg"

tomwer/gui/visualization/reconstructionparameters.py

@@ -160,15 +160,23 @@ class ReconstructionParameters(qt.QWidget):
         # voxel size can be stored as pixel size (old version) or voxel size (new version)
         recons_params = metadata.get("processing_options", {}).get("reconstruction", {})
         voxel_size_cm = recons_params.get("voxel_size_cm", None)
+
         # now voxel size is expected to be a tuple of three elements
         if voxel_size_cm is not None:
             voxel_size_cm = voxel_size_cm[0]
+            # FIXME: load_ini seems to fail to remove some char like '(' or ')'... to be fixed or investigate
+            # simplest might be to filter those when dumping it to text file... ??? or to handle those at silx level
+            if isinstance(voxel_size_cm, str):
+                for char_to_ignore in (" ", "(", ")", "[", "]"):
+                    voxel_size_cm = voxel_size_cm.replace(char_to_ignore, "")
         else:
             # backward compatibility with old volume
             voxel_size_cm = recons_params.get("pixel_size_cm", None)
         if voxel_size_cm is not None:
             voxel_size_cm = f"{float(voxel_size_cm):.8}"
-        self._pixelSizeQLE.setText(voxel_size_cm if voxel_size_cm is not None else "")
+        self._pixelSizeQLE.setText(
+            str(voxel_size_cm) if voxel_size_cm is not None else ""
+        )
 
     def _setCor(self, metadata: dict):
         cor = (

tomwer/gui/visualization/volumeviewer.py

@@ -357,6 +357,8 @@ class VolumeViewer(qt.QMainWindow):
                 self._set_volume(data)
             # set reconstruction parameters
             try:
+                # warning: limitation expected for .vol as it gets two configuration file. The default one is vol.info and does not contains
+                # any of the metadata 'distance', 'pixel size'... but it is here for backward compatiblity
                 self._reconsWidget.setVolumeMetadata(
                     volume.metadata or volume.load_metadata()
                 )

tomwer/resources/gui/icons/esrf_1.svg

@@ -0,0 +1,307 @@
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+
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+   height="48"
+   viewBox="0 0 12.7 12.7"
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+   id="svg911"
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+   inkscape:version="1.2.2 (b0a8486541, 2022-12-01)"
+   sodipodi:docname="esrf_1.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:xlink="http://www.w3.org/1999/xlink"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg"><sodipodi:namedview
+     id="namedview913"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
+     inkscape:showpageshadow="2"
+     inkscape:pageopacity="0.0"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1"
+     inkscape:document-units="mm"
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+     inkscape:zoom="6.7277216"
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+     inkscape:window-width="1920"
+     inkscape:window-height="1131"
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+       id="image1040"
+       x="-3.5774627"
+       y="-0.34973973"
+       inkscape:highlight-color="#0a51c2" /></g></svg>

tomwer/resources/gui/icons/triangle.svg

@@ -0,0 +1,80 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   width="48"
+   height="48"
+   viewBox="0 0 12.7 12.7"
+   version="1.1"
+   id="svg1097"
+   inkscape:version="1.2.2 (b0a8486541, 2022-12-01)"
+   sodipodi:docname="triangle.svg"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:svg="http://www.w3.org/2000/svg">
+  <sodipodi:namedview
+     id="namedview1099"
+     pagecolor="#ffffff"
+     bordercolor="#000000"
+     borderopacity="0.25"
+     inkscape:showpageshadow="2"
+     inkscape:pageopacity="0.0"
+     inkscape:pagecheckerboard="0"
+     inkscape:deskcolor="#d1d1d1"
+     inkscape:document-units="mm"
+     showgrid="false"
+     inkscape:zoom="9.5144352"
+     inkscape:cx="29.166208"
+     inkscape:cy="27.852415"
+     inkscape:window-width="1920"
+     inkscape:window-height="1163"
+     inkscape:window-x="1920"
+     inkscape:window-y="0"
+     inkscape:window-maximized="1"
+     inkscape:current-layer="layer1" />
+  <defs
+     id="defs1094" />
+  <g
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer"
+     id="layer1">
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 1.8939624,10.526614 10.57789,10.508604 10.61321,2.0330588 Z"
+       id="path1281" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 4.5730925,8.0439775 5.0764382,8.5595639"
+       id="path1381-3" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 5.5291259,7.0902652 6.0324716,7.6058516"
+       id="path1381-6" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 6.5287393,6.2125496 7.032085,6.728136"
+       id="path1381-7" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 7.4875733,5.2270671 7.990919,5.7426535"
+       id="path1381-5" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 8.3428853,4.4034115 8.846231,4.9189979"
+       id="path1381-35" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 7.3583237,9.2113359 9.4546511,9.2107622 9.4437729,6.976487 Z"
+       id="path1283"
+       sodipodi:nodetypes="cccc" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="M 3.5387896,9.0166385 4.0421353,9.5322249"
+       id="path1381" />
+    <path
+       style="fill:#ffffff;stroke:#000000;stroke-width:0.4;stroke-linejoin:round"
+       d="m 9.1315815,3.5812101 0.503346,0.5155864"
+       id="path1381-62" />
+  </g>
+</svg>

tomwer/version.py

@@ -79,7 +79,7 @@ MAJOR = 1
 MINOR = 2
 MICRO = 0
 RELEV = "alpha"  # <16
-SERIAL = 2  # <16
+SERIAL = 4  # <16
 
 date = __date__
 

{tomwer-1.2.0a2.dist-info → tomwer-1.2.0a4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tomwer
-Version: 1.2.0a2
+Version: 1.2.0a4
 Summary: "tomography workflow tools"
 Home-page: https://gitlab.esrf.fr/tomotools/tomwer
 Author: data analysis unit