[edf2nx] add options to provide `sample_name`, `title`, `instrument_name` and `source_name`

nxtomomill/app/edf2nx.py

@@ -59,8 +59,6 @@ Application to convert a tomo dataset written in edf into and hdf5/nexus file.
                             y translation key in EDF HEADER
       --z_trans_key Z_TRANS_KEY
                             z translation key in EDF HEADER
-
-
 """
 
 __authors__ = ["C. Nemoz", "H. Payno", "A.Sole"]
@@ -70,6 +68,8 @@ __date__ = "16/01/2020"
 
 import argparse
 import logging
+
+from nxtomomill.converter.hdf5.acquisition.baseacquisition import SourceType
 from nxtomomill import utils
 from nxtomomill import converter
 from nxtomomill.utils import Progress
@@ -143,6 +143,15 @@ def main(argv):
     parser.add_argument(
         "--z_trans_key", default=EDF_Z_TRANS, help="z translation key in EDF HEADER"
     )
+    parser.add_argument("--sample_name", default=None, help="name of the sample")
+    parser.add_argument("--title", default=None, help="title")
+    parser.add_argument("--instrument_name", default=None, help="instrument name used")
+    parser.add_argument("--source_name", default="ESRF", help="name of the source used")
+    parser.add_argument(
+        "--source_type",
+        default=SourceType.SYNCHROTRON_X_RAY_SOURCE,
+        help="type of the source used",
+    )
 
     options = parser.parse_args(argv[1:])
 
@@ -167,6 +176,11 @@ def main(argv):
         file_extension=options.file_extension,
         file_keys=file_keys,
         progress=Progress(""),
+        sample_name=options.sample_name,
+        title=options.title,
+        instrument_name=options.instrument_name,
+        source_name=options.source_name,
+        source_type=options.source_type,
     )
 
 

nxtomomill/converter/edf/edfconverter.py

@@ -35,6 +35,9 @@ __date__ = "27/11/2020"
 
 
 from collections import namedtuple
+from typing import Optional
+
+from nxtomomill.converter.hdf5.acquisition.baseacquisition import SourceType
 from nxtomomill import utils
 from nxtomomill.utils import ImageKey
 from nxtomomill.converter.version import version as converter_version
@@ -98,6 +101,11 @@ def edf_to_nx(
     file_extension: str,
     file_keys: EDFFileKeys = DEFAULT_EDF_KEYS,
     progress=None,
+    sample_name: Optional[str] = None,
+    title: Optional[str] = None,
+    instrument_name: Optional[str] = None,
+    source_name: Optional[str] = None,
+    source_type: Optional[SourceType] = None,
 ) -> tuple:
     """
     Convert an edf file to a nexus file.
@@ -108,6 +116,11 @@ def edf_to_nx(
     :param file_extension:
     :param file_keys:
     :param progress:
+    :param Optional[str] sample_name: name of the sample
+    :param Optional[str] title: dataset title
+    :param Optional[str] instrument_name: name of the instrument used
+    :param Optional[str] source_name: name of the source (most likely ESRF)
+    :param Optional[str] source_type: type of the source (most likely "Synchrotron X-ray Source")
     :return: (nexus_file, entry)
     :rtype:tuple
     """
@@ -121,6 +134,9 @@ def edf_to_nx(
     )
     _logger.info("Output file will be " + fileout_h5)
 
+    if source_type is not None:
+        source_type = SourceType.from_value(source_type)
+
     DARK_ACCUM_FACT = True
     with HDF5File(fileout_h5, "w") as h5d:
         proj_urls = scan.get_proj_urls(scan=scan.path)
@@ -212,7 +228,26 @@ def edf_to_nx(
             dtype=numpy.int32,
         )
 
-        h5d["/entry/sample/name"] = os.path.basename(scan.path)
+        h5d["/entry/title"] = (
+            title if title is not None else os.path.basename(scan.path)
+        )
+
+        if sample_name is None:
+            try:
+                sample_name = os.path.abspath(scan.path).split(os.sep)[-3:]
+            except:
+                sample_name = "unknow"
+        h5d["/entry/sample/name"] = sample_name
+        if instrument_name is not None:
+            instrument_grp = h5d["/entry"].require_group("instrument")
+            instrument_grp["name"] = instrument_name
+
+        if source_name is not None:
+            source_grp = h5d["/entry/instrument"].require_group("source")
+            source_grp["name"] = source_name
+        if source_type is not None:
+            source_grp = h5d["/entry/instrument"].require_group("source")
+            source_grp["type"] = source_type.value
 
         proj_angle = scan.scan_range / scan.tomo_n
 
@@ -551,6 +586,9 @@ def edf_to_nx(
         h5d["/entry/instrument/detector/data"].attrs["interpretation"] = u"image"
         h5d["/entry/sample"].attrs["NX_class"] = u"NXsample"
         h5d["/entry/definition"] = "NXtomo"
+        source_grp = h5d["/entry/instrument"].get("source", None)
+        if source_grp is not None and "NX_class" not in source_grp.attrs:
+            source_grp.attrs["NX_class"] = "NXsource"
 
         h5d.flush()