Merge branch 'handle_zserie_grp' into 'master'

Handle zserie grp

See merge request !39

CHANGELOG.rst

 Change Log
 ==========
 
+0.5.0: XXXX/YY/ZZ
+-----------------
+
+* esrf
+    * TomoScanBase: add properties `sequence_name`, `sample_name` and `group_size`
+    * utils: add the concept of groups. A group for example is a set of sequences defining a zseries
+
 0.4.0: 2020/11/09
 -----------------
 

tomoscan/esrf/__init__.py

@@ -28,3 +28,6 @@ __license__ = "MIT"
 __date__ = "09/08/2018"
 
 TYPES = ["EDF", "HDF5"]
+
+from .hdf5scan import HDF5TomoScan
+from .edfscan import EDFTomoScan

tomoscan/esrf/hdf5scan.py

@@ -89,6 +89,14 @@ class HDF5TomoScan(TomoScanBase):
 
     _ROTATION_ANGLE_PATH = "sample/rotation_angle"
 
+    _SAMPLE_PATH = "sample"
+
+    _NAME_PATH = "sample/name"
+
+    _GRP_SIZE_ATTR = "group_size"
+
+    _SAMPLE_NAME_PATH = "sample/sample_name"
+
     _X_TRANS_PATH = "sample/x_translation"
 
     _Y_TRANS_PATH = "sample/y_translation"
@@ -160,7 +168,9 @@ class HDF5TomoScan(TomoScanBase):
                     "unable to find a valid entry for %s" % self.master_file
                 )
         # for now the default entry is 1_tomo but should change with time
-
+        self._name = None
+        self._sample_name = None
+        self._grp_size = None
         # data caches
         self._projections_compacted = None
         self._flats = None
@@ -355,6 +365,44 @@ class HDF5TomoScan(TomoScanBase):
     def entry(self) -> str:
         return self._entry
 
+    @property
+    def sequence_name(self):
+        """Return the sequence name"""
+        if self._name is None and self.master_file and os.path.exists:
+            self._check_hdf5scan_validity()
+            with HDF5File(self.master_file, "r") as h5_file:
+                if self._NAME_PATH in h5_file[self._entry]:
+                    self._name = h5py_read_dataset(
+                        h5_file[self._entry][self._NAME_PATH]
+                    )
+        return self._name
+
+    @property
+    @docstring(TomoScanBase.projections)
+    def sample_name(self):
+        if self._sample_name is None and self.master_file and os.path.exists:
+            self._check_hdf5scan_validity()
+            with HDF5File(self.master_file, "r") as h5_file:
+                if self._SAMPLE_NAME_PATH in h5_file[self._entry]:
+                    self._sample_name = h5py_read_dataset(
+                        h5_file[self._entry][self._SAMPLE_NAME_PATH]
+                    )
+        return self._sample_name
+
+    @property
+    @docstring(TomoScanBase.projections)
+    def group_size(self):
+        if self._grp_size is None and self.master_file and os.path.exists:
+            self._check_hdf5scan_validity()
+            with HDF5File(self.master_file, "r") as h5_file:
+                if self._SAMPLE_PATH in h5_file[self._entry]:
+                    grp = h5_file[self._entry][self._SAMPLE_PATH]
+                    if self._GRP_SIZE_ATTR in grp.attrs:
+                        self._grp_size = h5py_read_dataset(
+                            grp.attrs[self._GRP_SIZE_ATTR]
+                        )
+        return self._grp_size
+
     @property
     @docstring(TomoScanBase.projections)
     def projections(self) -> typing.Union[dict, None]:

tomoscan/esrf/utils.py

@@ -31,8 +31,13 @@ __date__ = "10/10/2019"
 import os
 import fabio
 from silx.io.url import DataUrl
+from tomoscan.scanbase import TomoScanBase
 from typing import Union
+from typing import Iterable
 import numpy
+import logging
+
+_logger = logging.getLogger(__name__)
 
 
 def get_parameters_frm_par_or_info(file_: str) -> dict:
@@ -172,3 +177,71 @@ def get_compacted_dataslices(urls):
             )
         )
     return res
+
+
+def from_sequences_to_grps(scans: Iterable) -> tuple:
+    """
+    create group with the same sample name
+
+    :param Iterable scans:
+    :return: tuple of group of scans
+    """
+    grps = {}
+    for scan in scans:
+        if not isinstance(scan, TomoScanBase):
+            raise TypeError("Elements are expected to be instance of " "TomoScanBase")
+        if scan.sample_name in grps:
+            grps[scan.sample_name].append(scan)
+        else:
+            grps[scan.sample_name] = [
+                scan,
+            ]
+    return tuple(grps.values())
+
+
+def check_grp_is_valid(scans: Iterable):
+    """
+    Insure the provided group of scan is valid. Otherwise raise an error
+
+    :param Iterable scans: group of TomoScanBAse to check
+    """
+    l_scans = set()
+    for scan in scans:
+        if not isinstance(scan, TomoScanBase):
+            raise TypeError("Elements are expected to be instance of " "TomoScanBase")
+        if scan in l_scans:
+            raise ValueError("{} is present at least twice")
+        elif len(l_scans) > 0:
+            if list(l_scans)[0].sample_name != scan.sample_name:
+                raise ValueError(
+                    "{} and {} are from two different sample".format(scan, l_scans)
+                )
+        l_scans.add(scan)
+
+
+def grp_is_complete(scans: Iterable) -> bool:
+    """
+    Insure the provided group of scan is valid. Otherwise raise an error
+
+    :param Iterable scans: group of TomoScanBAse to check
+    :return: True if the group is complete
+    :rtype: bool
+    """
+    if len(scans) == 0:
+        return True
+    try:
+        check_grp_is_valid(scans=scans)
+    except Exception as e:
+        _logger.error("provided group is invalid. {}".format(e))
+    else:
+        group_size = list(scans)[0].group_size
+        if group_size is None:
+            _logger.warning("No information found regarding group size")
+            return True
+        elif group_size == len(scans):
+            return True
+        elif group_size < len(scans):
+            _logger.warning("more scans found than group_size")
+            return True
+        else:
+            return False

tomoscan/scanbase.py

@@ -299,6 +299,22 @@ class TomoScanBase:
         """Parse the root folder and files to update informations"""
         raise NotImplementedError("Base class")
 
+    @property
+    def sequence_name(self):
+        """Return the sequence name"""
+        raise NotImplementedError("Base class")
+
+    @property
+    def sample_name(self):
+        """Return the sample name"""
+        raise NotImplementedError("Base class")
+
+    @property
+    def group_size(self):
+        """Used in the case of zseries for example. Return the number of
+        sequence expected on the acquisition"""
+        raise NotImplementedError("Base class")
+
     def to_dict(self) -> dict:
         """