tomwer 1.3.27__py3-none-any.whl → 1.4.0rc0__py3-none-any.whl

tomwer/core/scan/edfscan.py

@@ -1,32 +1,4 @@
-# coding: utf-8
-# /*##########################################################################
-# Copyright (C) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#############################################################################*/
-
-
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "09/08/2018"
-
+from __future__ import annotations
 
 import functools
 import logging
@@ -35,14 +7,15 @@ import re
 from collections import OrderedDict
 from glob import glob
 from math import ceil
-from typing import Optional
 import pathlib
 from datetime import datetime
 
 import fabio
 import numpy
+from tqdm import tqdm
 from processview.core.dataset import DatasetIdentifier
 from silx.io.url import DataUrl
+
 from tomoscan.esrf.identifier.edfidentifier import (
     EDFTomoScanIdentifier as _EDFTomoScanIdentifier,
 )
@@ -54,7 +27,6 @@ from tomwer.core.process.reconstruction.darkref.settings import (
     DARKHST_PREFIX,
     REFHST_PREFIX,
 )
-from tomwer.core.progress import Progress
 from tomwer.utils import docstring
 
 from .scanbase import TomwerScanBase
@@ -93,7 +65,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
     """
     Class used to represent a tomography acquisition with hdf5 files.
 
-    :param Union[str, None] scan: path of the scan
+    :param scan: path of the scan
     """
 
     def __init__(self, scan, overwrite_proc_file=False, update=True):
@@ -130,7 +102,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
     @staticmethod
     def is_tomoscan_dir(
         directory: str,
-        dataset_basename: Optional[str] = None,
+        dataset_basename: str | None = None,
         src_pattern=None,
         dest_pattern=None,
         **kwargs,
@@ -175,15 +147,14 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
         """
         Check if the given directory is holding an acquisition
 
-        :param str directory: directory we want to check
-        :param str src_pattern: buffer name pattern ('lbsram')
+        :param directory: directory we want to check
+        :param src_pattern: buffer name pattern ('lbsram')
         :param dest_pattern: output pattern (''). Needed because some
                              acquisition can split the file produce between
                              two directories. This is the case for edf,
                              where .info file are generated in /data/dir
                              instead of /lbsram/data/dir
         :return: does the given directory contains any acquisition
-        :rtype: bool
         """
         aux = directory.split(os.path.sep)
         info_name = os.path.join(directory, aux[-1] + EDFTomoScan.INFO_EXT)
@@ -196,7 +167,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
         """
         Apply the flat field correction on the given data.
 
-        :param numpy.ndarray data: radio to correct
+        :param data: radio to correct
         :return numpy.ndarray: corrected data
         """
         dark = self.getDark()
@@ -227,7 +198,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
         * .vol files
 
         :param scanID: is the path to the folder of acquisition
-        :param bool withIndex: if False then return a list of slices otherwise
+        :param withIndex: if False then return a list of slices otherwise
             return a dict with the index of the slice reconstructed.
         """
 
@@ -297,7 +268,6 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
         """
 
         :return: scheme to read url
-        :rtype: str
         """
         return "fabio"
 
@@ -309,11 +279,8 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
         extract the sinogram from projections
 
         :param line: which sinogram we want
-        :type: int
         :param subsampling: subsampling to apply if any. Allows to skip some io
-        :type: int
         :return: sinogram from the radio lines
-        :rtype: numpy.array
         """
         _logger.info(
             f"compute sinogram for line {line} of {self.path} (subsampling: {subsampling})"
@@ -329,27 +296,26 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
             proj_sort = list(proj_urls.keys())
             proj_sort = list(filter(lambda x: not isinstance(x, str), proj_sort))
             proj_sort.sort()
-            advancement = Progress(
-                name=f"compute sinogram for {os.path.basename(self.path)}, line={line}, sampling={subsampling}"
+            advancement = tqdm(
+                desc=f"compute sinogram for {os.path.basename(self.path)}, line={line}, sampling={subsampling}"
             )
-            advancement.setMaxAdvancement(len(proj_sort))
+            advancement.total = len(proj_sort)
             for i_proj, proj in enumerate(proj_sort):
                 if i_proj % subsampling == 0:
                     url = proj_urls[proj]
                     radio = get_data(url)
                     radio = self.data_flat_field_correction(radio)
                     sinogram[i_proj // subsampling] = radio[line]
-                advancement.increaseAdvancement(1)
+                advancement.update()
             return sinogram
 
     @functools.lru_cache(maxsize=3)
-    def getFlat(self, index=None):
+    def getFlat(self, index: int | None = None):
         """
         If projectionI is not requested then return the mean value. Otherwise
         return the interpolated value for the requested projection.
 
-        :param Union[int,None] index: index of the projection for which we want
-                                      the flat
+        :param index: index of the projection for which we want the flat
         :return: Flat field value or None if can't deduce it
         """
         data = self._extractFromOneFile("refHST.edf", what="flat")
@@ -497,7 +463,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
     def get_index_reconstructed(reconstructionFile, scanID):
         """Return the slice reconstructed of a file from her name
 
-        :param str reconstructionFile: the name of the file
+        :param reconstructionFile: the name of the file
         """
         folderBasename = os.path.basename(scanID)
         if reconstructionFile.endswith(".edf") and reconstructionFile.startswith(
@@ -587,7 +553,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
         return analyzer
 
     @docstring(TomwerScanBase)
-    def scan_dir_name(self) -> Optional[str]:
+    def scan_dir_name(self) -> str | None:
         """for 'this/is/my/acquisition' returns 'acquisition'"""
         if self.path is not None:
             return self.path.split(os.sep)[-1]
@@ -595,7 +561,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
             return None
 
     @docstring(TomwerScanBase)
-    def scan_basename(self) -> Optional[str]:
+    def scan_basename(self) -> str | None:
         """for 'this/is/my/acquisition' returns 'acquisition'"""
         if self.path is not None:
             return self.path
@@ -603,7 +569,7 @@ class EDFTomoScan(_tsEDFTomoScan, TomwerScanBase):
             return None
 
     @docstring(TomwerScanBase)
-    def scan_parent_dir_basename(self) -> Optional[str]:
+    def scan_parent_dir_basename(self) -> str | None:
         if self.path is not None:
             try:
                 return os.path.dirname(self.path)

tomwer/core/scan/hdf5scan.py

@@ -9,7 +9,7 @@ class HDF5TomoScanIdentifier(NXtomoScanIdentifier):
             type_="class",
             reason="improve readibility",
             since_version="1.3",
-            replacement="VolumeSymbolicLinkTask",
+            replacement="NXtomoScanIdentifier",
         )
         super().__init__(metadata, *args, **kwargs)
 
@@ -21,6 +21,6 @@ class HDF5TomoScan(NXtomoScan):
             type_="class",
             reason="improve readibility",
             since_version="1.3",
-            replacement="VolumeSymbolicLinkTask",
+            replacement="NXtomoScan",
         )
         super().__init__(scan, entry, index, overwrite_proc_file)

tomwer/core/scan/nxtomoscan.py

@@ -1,32 +1,4 @@
-# coding: utf-8
-# /*##########################################################################
-# Copyright (C) 2016 European Synchrotron Radiation Facility
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#
-#############################################################################*/
-
-
-__authors__ = ["H.Payno"]
-__license__ = "MIT"
-__date__ = "09/08/2018"
-
+from __future__ import annotations
 
 import functools
 import io
@@ -35,18 +7,19 @@ import logging
 import os
 import pathlib
 from datetime import datetime
-from typing import Optional
 from urllib.parse import urlparse
 
 import h5py
 from processview.core.dataset import DatasetIdentifier
 from silx.io.utils import open as open_hdf5
+from silx.io.url import DataUrl
 from tomoscan.esrf.identifier.hdf5Identifier import (
     NXtomoScanIdentifier as _NXtomoScanIdentifier,
 )
 from tomoscan.esrf.identifier.url_utils import UrlSettings, split_path, split_query
 from tomoscan.esrf.scan.nxtomoscan import NXtomoScan as _tsNXtomoScan
 from nxtomo.nxobject.nxdetector import ImageKey
+from nxtomo.paths.nxtomo import get_paths as _get_nexus_paths
 
 from tomwer.utils import docstring
 from tomwer.core.scan.helicalmetadata import HelicalMetadata
@@ -102,16 +75,21 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
     For now several property of the acquisition is accessible thought a getter
     (like get_scan_range) and a property (scan_range).
 
-    This is done to be compliant with TomoBase instanciation. But his will be
+    This is done to be compliant with TomoBase instantiation. But his will be
     replace progressively by properties at the 'TomoBase' level
 
     :param scan: scan directory or scan masterfile.h5
-    :type: Union[str,None]
     """
 
     _TYPE = "hdf5"
 
-    def __init__(self, scan, entry, index=None, overwrite_proc_file=False):
+    def __init__(
+        self,
+        scan: str | None,
+        entry: str | None,
+        index: int | None = None,
+        overwrite_proc_file: bool = False,
+    ):
         TomwerScanBase.__init__(self)
         _tsNXtomoScan.__init__(self, scan=scan, entry=entry, index=index)
         # speed up for now, avoid to run check by default
@@ -196,16 +174,14 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
 
         Check if the given directory is holding an acquisition
 
-        :param str directory: directory we want to check
-        :param str src_pattern: buffer name pattern ('lbsram')
+        :param directory: directory we want to check
+        :param src_pattern: buffer name pattern ('lbsram')
         :param dest_pattern: output pattern (''). Needed because some
                              acquisition can split the file produce between
                              two directories. This is the case for edf,
                              where .info file are generated in /data/dir
                              instead of /lbsram/data/dir
-        :type: str
         :return: does the given directory contains any acquisition
-        :rtype: bool
         """
         master_file = os.path.join(directory, os.path.basename(directory))
         if os.path.exists("master_file.hdf5"):
@@ -222,7 +198,7 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         Check if the acquisition have been aborted. In this case the directory
         should contain a [scan].abo file
 
-        :param str src_pattern: buffer name pattern ('lbsram')
+        :param src_pattern: buffer name pattern ('lbsram')
         :param dest_pattern: output pattern (''). Needed because some
                              acquisition can split the file produce between
                              two directories. This is the case for edf,
@@ -274,13 +250,12 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         if not os.path.exists(self.master_file):
             return
         _tsNXtomoScan.update(self)
-        self.reconstructions = self.get_reconstructions_urls()
+        self.reconstructions = self.get_reconstructed_slices()
 
     def _get_scheme(self):
         """
 
         :return: scheme to read url
-        :rtype: str
         """
         return "silx"
 
@@ -295,11 +270,8 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         extract the sinogram from projections
 
         :param line: which sinogram we want
-        :type: int
         :param subsampling: subsampling to apply if any. Allows to skip some io
-        :type: int
         :return: sinogram from the radio lines
-        :rtype: numpy.array
         """
         return _tsNXtomoScan.get_sinogram(
             self,
@@ -376,7 +348,7 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
                 return None, None
             else:
                 self._last_flat_index = None
-                self._first_serie_flat_index = None
+                self._first_series_flat_index = None
                 for flat_index in self.flats:
                     if self._last_flat_index is None:
                         self._last_flat_index = flat_index
@@ -387,11 +359,11 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
                         return self._last_flat_index, flat_index
             return None, None
 
-        first_serie_index, second_serie_index = get_first_two_ff_indexes()
-        if first_serie_index is None:
+        first_series_index, second_series_index = get_first_two_ff_indexes()
+        if first_series_index is None:
             return 0
-        elif second_serie_index is not None:
-            return second_serie_index - first_serie_index - 1
+        elif second_series_index is not None:
+            return second_series_index - first_series_index - 1
         else:
             return 0
 
@@ -444,9 +416,8 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         """
         Check if the grp is an nx detector
 
-        :param h5py.Group grp:
+        :param grp:
         :return: True if this is the definition of a group
-        :rtype: bool
         """
         if hasattr(grp, "attrs"):
             if "NX_class" in grp.attrs and grp.attrs["NX_class"] == "NXdetector":
@@ -482,7 +453,7 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         )
 
     @docstring(TomwerScanBase)
-    def scan_dir_name(self) -> Optional[str]:
+    def scan_dir_name(self) -> str | None:
         """for 'this/is/my/file.h5' returns 'my'"""
         if self.master_file is not None:
             return os.path.dirname(self.master_file).split(os.sep)[-1]
@@ -509,9 +480,9 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
         else:
             return None
 
-    def get_proposal_name(self) -> Optional[str]:
+    def get_proposal_name(self) -> str | None:
         if self._proposal_name is None and self.master_file is not None:
-            bliss_raw_data_files = self.get_bliss_orginal_files() or ()
+            bliss_raw_data_files = self.get_bliss_original_files() or ()
             bliss_raw_data_file = (
                 bliss_raw_data_files[0] if len(bliss_raw_data_files) > 0 else None
             )
@@ -529,6 +500,27 @@ class NXtomoScan(_tsNXtomoScan, TomwerScanBase):
                     self._proposal_name = strips[3]
                 else:
                     _logger.warning(
-                        "this doesn't looks like a bliss file aquired at the ESRF. Unable to find proposal name"
+                        "this doesn't looks like a bliss file acquired at the ESRF. Unable to find proposal name"
                     )
         return self._proposal_name
+
+    def get_detector_url(self) -> DataUrl | None:
+        """
+        compute and return the url where the detector data can be found
+        """
+        if self.master_file is None:
+            return None
+        else:
+            nexus_paths = _get_nexus_paths(version=self.nexus_version)
+            return DataUrl(
+                file_path=self.master_file,
+                data_path="/".join(
+                    (
+                        self.entry,
+                        nexus_paths.INSTRUMENT_PATH,
+                        nexus_paths.nx_instrument_paths.DETECTOR_PATH,
+                        nexus_paths.nx_instrument_paths.DATA,
+                    )
+                ),
+                scheme="silx",
+            )