Merge branch 'beamline_readers'

XraySpectroscopy · Jul 26, 2024 · d87289c · d87289c
2 parents 8a99ec5 + 9ffb4fa
commit d87289c
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Showing 6 changed files with 22 additions and 19 deletions.
diff --git a/conversion_examples/Fe_XDIFiles/fe_xas_nexus.h5 b/conversion_examples/Fe_XDIFiles/fe_xas_nexus.h5
diff --git a/conversion_examples/Fe_XDIFiles/make_xas.py b/conversion_examples/Fe_XDIFiles/make_xas.py
@@ -67,7 +67,7 @@ def xdi2nexus(filename, nxroot, entry_name='entry',
         preline = f"({preline})*energy(-{dat.nvict})"
 
     proc = ["processing done with xraylarch version 0.9.80",
-            f"    larch.xafs.pre_edge(data, {kwargs})",
+            f"larch.xafs.pre_edge(data, {kwargs})",
             "using 'data' from arrays in rawdata",
             "energy = data[:,0]      # column 1: energy (eV)",
             "itrans = data[:, 2]     # column 3: transmitted beam intensity",
@@ -103,17 +103,20 @@ def xdi2nexus(filename, nxroot, entry_name='entry',
     root['process'] = nexus.NXprocess(program='xraylarch', version='0.9.80',
                                       notes=notes)
 
-
-
     # rawdata
-    root['rawdata'] = rawdata
-    root['rawdata'].attrs['column_labels'] = json.dumps(["energy", "intensity", "itrans", "i0"])
-    root['rawdata'].attrs['data_collector'] = 'Matthew Newville'
-    root['rawdata'].attrs['filename'] = filename
+    array_labels = json.dumps(["energy", "intensity", "itrans", "i0"])
+    root['rawdata'] = rawdata.T
+    root['rawdata'].attrs['array_labels'] = array_labels
+
 
+    root['reference'] = 'None'
 
     # scan
     scan = root['scan'] = nexus.NXcollection()
+    scan.attrs['data_collector'] = 'Matthew Newville'
+    scan.attrs['filename'] = filename
+
+
     scan.headers = json.dumps(dat.attrs)
 
     for key, val in dat.attrs['scan'].items():

diff --git a/conversion_examples/KEK_PFdata/Fe_XAS_PF9A_nexus.h5 b/conversion_examples/KEK_PFdata/Fe_XAS_PF9A_nexus.h5
diff --git a/conversion_examples/KEK_PFdata/make_xas.py b/conversion_examples/KEK_PFdata/make_xas.py
@@ -8,8 +8,6 @@
 from larch.utils import gformat
 
 
-
-
 PLANCK_HC = 12398.419843320027
 DEG2RAD = 0.017453292519943295
 
@@ -94,7 +92,7 @@ def kekpf2nexus(filename, nxroot, entry_name='entry',   metadata=None):
         preline = f"({preline})*energy(-{dat.nvict})"
 
     proc = ["processing done with xraylarch version 0.9.80",
-            f"    larch.xafs.pre_edge(data, {kwargs})",
+            f"larch.xafs.pre_edge(data, {kwargs})",
             "energy = col1    # column 1: energy (eV)",
             "ifluor = col3    # column 3: fluorescence intensity",
             "i0     = col4    # column 4: incident beam intensity",
@@ -144,15 +142,16 @@ def kekpf2nexus(filename, nxroot, entry_name='entry',   metadata=None):
                                       notes=notes)
 
     # rawdata
-    root['rawdata'] = np.array(coldata)
-    root['rawdata'].attrs['column_labels'] = json.dumps(array_labels)
-    root['rawdata'].attrs['data_collector'] = 'KEK PF BL9A'
-    root['rawdata'].attrs['filename'] = filename
+    root['rawdata'] = np.array(coldata).T
+    root['rawdata'].attrs['array_labels'] = json.dumps(array_labels)
 
+    root['reference'] = 'None'
 
     # scan
     scan = root['scan'] = nexus.NXcollection()
     scan.headers = json.dumps(meta)
+    scan.data_collector = 'KEK PF BL9A'
+    scan.filename = filename
 
     if 'scan' in meta:
         for key, val in meta['scan'].items():

diff --git a/conversion_examples/MultiElementFluor/V_XANES_nexus.h5 b/conversion_examples/MultiElementFluor/V_XANES_nexus.h5
diff --git a/conversion_examples/MultiElementFluor/make_xas.py b/conversion_examples/MultiElementFluor/make_xas.py
@@ -120,7 +120,7 @@ def xdi2nexus(filename, nxroot, entry_name='entry',
         dtc = "with deadtime corection from columns in the data"
     nd = len(coldata)
     proc = ["processing done with xraylarch version 0.9.80",
-            f"    larch.xafs.pre_edge(data, {kwargs})",
+            f"larch.xafs.pre_edge(data, {kwargs})",
             f"using col1..col{nd} for {nd} from arrays in rawdata",
             "energy = col1    # column 1: energy (eV)",
             "i0     = col4    # column 4: incident beam intensity",
@@ -171,15 +171,16 @@ def xdi2nexus(filename, nxroot, entry_name='entry',
                                       notes=notes)
 
     # rawdata
-    root['rawdata'] = np.array(coldata)
-    root['rawdata'].attrs['column_labels'] = json.dumps(array_labels)
-    root['rawdata'].attrs['data_collector'] = 'Matthew Newville'
-    root['rawdata'].attrs['filename'] = filename
+    root['rawdata'] = np.array(coldata).T
+    root['rawdata'].attrs['array_labels'] = json.dumps(array_labels)
 
+    root['reference'] = 'None'
 
     # scan
     scan = root['scan'] = nexus.NXcollection()
     scan.headers = json.dumps(meta)
+    scan.data_collector = 'Tony Lanzirotti'
+    scan.filename = filename
 
     for key, val in meta['scan'].items():
         setattr(scan, key, val)