Merge pull request #130 from aglavic/fix_nxs

NeXus creation fails when dictrionary of ORSO objects is present
reflectivity · Jul 1, 2024 · 7eef00e · 7eef00e
2 parents c88ab4c + c529619
commit 7eef00e
Show file tree

Hide file tree

Showing 4 changed files with 168 additions and 12 deletions.
diff --git a/examples/prist5_10K_m_025.Rqz.ort b/examples/prist5_10K_m_025.Rqz.ort
@@ -0,0 +1,124 @@
+# # ORSO reflectivity data file | 1.0 standard | YAML encoding | https://www.reflectometry.org/
+# data_source:
+#   owner:
+#     name: Artur Glavic
+#     affiliation: null
+#     contact: b''
+#   experiment:
+#     title: Structural evolution of the CO2/Water interface
+#     instrument: Amor
+#     start_date: 2023-11-29T10:12:45
+#     probe: neutron
+#     facility: SINQ@PSI
+#     proposalID: '20230368'
+#   sample:
+#     name: prist4
+#     sample_parameters:
+#       tempMean: {magnitude: -9999.0}
+#     model:
+#       stack: vacuum | Al2O3 2 | Ti0.27Co0.73 9.3 | Si
+#   measurement:
+#     instrument_settings:
+#       incident_angle: {min: 0.0950000000000002, max: 1.495, unit: deg}
+#       wavelength: {min: 3.0, max: 12.0, unit: angstrom}
+#       mu: {magnitude: 0.25, unit: deg, comment: sample angle to referece direction}
+#       nu: {magnitude: 1.0450000000000002, unit: deg, comment: detector angle to referece
+#           direction}
+#     data_files:
+#     - file: raw/amor2023n000848.hdf
+#       timestamp: 2023-11-29T10:12:45
+#       amor_monitor: 1792.443302905
+#     scheme: angle- and energy-dispersive
+#     references: []
+#     amor_monitor: 1792.443302905
+# reduction:
+#   software: {name: eos, version: '2.0'}
+#   timestamp: 2023-11-29T10:57:48.480339
+#   computer: amor.psi.ch
+#   call: eos.py -a 0.04 -F 0.0093,0.0101 -n 848 prist5_10K_m_025
+# data_set: 0
+# columns:
+# - {name: Qz, unit: 1/angstrom, physical_quantity: normal momentum transfer}
+# - {name: R, unit: '', physical_quantity: specular reflectivity}
+# - {error_of: R, error_type: uncertainty, value_is: sigma}
+# - {error_of: Qz, error_type: resolution, value_is: sigma}
+# # Qz (1/angstrom)    R ()                   sR                     sQz                   
+2.1999999999999997e-03 4.7241193897215048e-03 4.7241193897215048e-03 1.9999999999999987e-04
+2.5999999999999999e-03 0.0000000000000000e+00 0.0000000000000000e+00 2.0000000000000009e-04
+3.0000000000000001e-03 4.9441079014990305e-03 2.8632759811688313e-03 2.0000000000000009e-04
+3.4000000000000002e-03 5.3957146642147798e-03 2.7033018099334193e-03 1.9999999999999987e-04
+3.8000000000000000e-03 1.1948517768746966e-02 3.7903477990210636e-03 2.0000000000000009e-04
+4.2000000000000006e-03 1.6302332669940297e-02 3.9723175648453228e-03 2.0000000000000009e-04
+4.5999999999999999e-03 2.2652164871650581e-02 4.5763672802481776e-03 2.0000000000000009e-04
+5.0000000000000001e-03 2.3020814468949415e-02 4.2537271133726200e-03 1.9999999999999966e-04
+5.4000000000000003e-03 2.7305557750665344e-02 4.4287009711273589e-03 2.0000000000000009e-04
+5.7999999999999996e-03 1.9457945835850306e-02 3.7817426451169783e-03 2.0000000000000009e-04
+6.2000000000000006e-03 2.7645506109865266e-02 4.2679939914090732e-03 2.0000000000000009e-04
+6.6000000000000000e-03 2.4223034347324195e-02 3.7655052701117517e-03 2.0000000000000009e-04
+7.0000000000000001e-03 2.8408308819418325e-02 3.7377941755602716e-03 1.9999999999999966e-04
+7.4000000000000003e-03 5.7460495308053604e-02 5.2154049057105455e-03 2.0000000000000009e-04
+7.7999999999999996e-03 1.4898833519509819e-01 7.5478984035617898e-03 2.0000000000000009e-04
+8.1999999999999990e-03 3.5204809294430212e-01 1.1146891694516669e-02 1.9999999999999966e-04
+8.6000000000000000e-03 5.3176577607895481e-01 1.3517251795319620e-02 1.9999999999999966e-04
+8.9999999999999993e-03 7.9145006465015877e-01 1.6276277463585134e-02 2.0000000000000052e-04
+9.3999999999999986e-03 9.6803310478461035e-01 1.7827487993063780e-02 1.9999999999999966e-04
+9.7999999999999997e-03 1.0324643310179094e+00 1.8104900945963596e-02 2.0000000000000052e-04
+1.0204081632653062e-02 6.2876616833212340e-01 1.3873373556929145e-02 2.0408163265306107e-04
+1.0620574760516453e-02 3.5069559151104790e-01 1.0136613757789808e-02 2.1241149521033023e-04
+1.1054067607884473e-02 2.3477751708069897e-01 8.1099626399286761e-03 2.2108135215768900e-04
+1.1505254040859348e-02 1.8964302712880826e-01 7.1805730148316446e-03 2.3010508081718756e-04
+1.1974856246608712e-02 1.4285208497806512e-01 6.0162249267477130e-03 2.3949712493217482e-04
+1.2463625889327434e-02 1.2188457497836602e-01 5.4352795853431970e-03 2.4927251778654805e-04
+1.2972345313381616e-02 1.0530945504618572e-01 5.0275179459601553e-03 2.5944690626763297e-04
+1.3501828795560456e-02 8.0387950876579850e-02 4.1975562768255060e-03 2.7003657591120889e-04
+1.4052923848440476e-02 7.3136722795496253e-02 3.9582003984186967e-03 2.8105847696880976e-04
+1.4626512576948251e-02 6.1298419781514651e-02 3.4783001152817426e-03 2.9253025153896592e-04
+1.5223513090293080e-02 6.2409059365864682e-02 3.4798000624600761e-03 3.0447026180586197e-04
+1.5844880971529533e-02 5.6512800965543043e-02 3.2223775371921573e-03 3.1689761943059103e-04
+1.6491610807102167e-02 5.0440737935525240e-02 2.9021067247837801e-03 3.2983221614204389e-04
+1.7164737778820625e-02 5.0277525044171101e-02 2.8252864493045079e-03 3.4329475557641313e-04
+1.7865339320813300e-02 5.1689705097227867e-02 2.8118143416053952e-03 3.5730678641626538e-04
+1.8594536844111803e-02 5.3007618770583402e-02 2.7685413804410695e-03 3.7189073688223724e-04
+1.9353497531626573e-02 4.9070756677145402e-02 2.5677593751218504e-03 3.8706995063253133e-04
+2.0143436206386842e-02 4.6878831709663782e-02 2.4119133732668076e-03 4.0286872412773761e-04
+2.0965617276035284e-02 4.9199553772144550e-02 2.4276503561561644e-03 4.1931234552070561e-04
+2.1821356756689787e-02 5.2041112703109127e-02 2.4556151556737898e-03 4.3642713513379616e-04
+2.2712024379411822e-02 4.9251781726106690e-02 2.3335505076022252e-03 4.5424048758823873e-04
+2.3639045782653120e-02 4.3172608947743572e-02 2.1138539656044499e-03 4.7278091565306109e-04
+2.4603904794189984e-02 3.8304327635500499e-02 1.9158755178575817e-03 4.9207809588380086e-04
+2.5608145806197739e-02 4.4442200106459967e-02 2.0186419327094269e-03 5.1216291612395451e-04
+2.6653376247267036e-02 3.9587001147536376e-02 1.8488058581743547e-03 5.3306752494534232e-04
+2.7741269155318757e-02 3.6677858215866437e-02 1.7473224966445143e-03 5.5482538310637659e-04
+2.8873565855535847e-02 3.7663512267048754e-02 1.7682821318945074e-03 5.7747131711071743e-04
+3.0052078747598535e-02 3.6755569252809664e-02 1.7350440273063527e-03 6.0104157495196979e-04
+3.1278694206684193e-02 3.8546394417761670e-02 1.7965558626918197e-03 6.2557388413368373e-04
+3.2555375602875386e-02 3.2866785139061716e-02 1.6217721152892931e-03 6.5110751205750897e-04
+3.3884166443809073e-02 3.1513196803753502e-02 1.6061232808323794e-03 6.7768332887618160e-04
+3.5267193645597203e-02 3.0280345918169513e-02 1.5885947028228238e-03 7.0534387291194475e-04
+3.6706670937254229e-02 2.5036982048446406e-02 1.4176844815086535e-03 7.3413341874508514e-04
+3.8204902404080934e-02 2.0831804563285421e-02 1.2803365468167761e-03 7.6409804808161980e-04
+3.9764286175676081e-02 1.9376976329704945e-02 1.2712203272554497e-03 7.9528572351352314e-04
+4.1387318264479181e-02 1.6729675515039004e-02 1.1715497338181137e-03 8.2774636528958404e-04
+4.3076596560988542e-02 1.3996303090353096e-02 1.0654383375290077e-03 8.6153193121977015e-04
+4.4834824992049299e-02 1.0621480384334052e-02 9.2468077823003954e-04 8.9669649984099042e-04
+4.6664817848867640e-02 7.8203324635251256e-03 8.0931024548367521e-04 9.3329635697735405e-04
+4.8569504291678570e-02 6.0428022894521575e-03 7.1838354133842033e-04 9.7139008583356848e-04
+5.0551933038277694e-02 4.0958929714843932e-03 5.8416704469953131e-04 1.0110386607655557e-03
+5.2615277243921690e-02 5.1115251619419473e-03 6.6580030308840434e-04 1.0523055448784409e-03
+5.4762839580408292e-02 2.0207116612746484e-03 4.1438660592314769e-04 1.0952567916081637e-03
+5.6998057522465770e-02 1.7115689314143780e-03 3.8529038925611664e-04 1.1399611504493146e-03
+5.9324508849913360e-02 8.4963058831312487e-04 2.7095330976641694e-04 1.1864901769982721e-03
+6.1745917374399620e-02 8.1421160351772355e-04 2.7251395576638693e-04 1.2349183474879948e-03
+6.4266158899885323e-02 8.9204238262309603e-05 8.9204238263225523e-05 1.2853231779977048e-03
+6.6889267426411256e-02 9.3397363465611626e-05 9.3397363464899779e-05 1.3377853485282282e-03
+6.9619441607081112e-02 4.0599169078880156e-04 2.0303208241886721e-04 1.3923888321416208e-03
+7.2461051468594620e-02 2.1832573520758229e-04 1.5439324988622013e-04 1.4492210293718943e-03
+7.5418645406088280e-02 1.2684339163878999e-04 1.2684339163797725e-04 1.5083729081217731e-03
+7.8496957463479650e-02 0.0000000000000000e+00 0.0000000000000000e+00 1.5699391492695891e-03
+8.1700914910968619e-02 0.0000000000000000e+00 0.0000000000000000e+00 1.6340182982193738e-03
+8.5035646131824488e-02 4.1657483226777538e-04 2.4090333523406435e-04 1.7007129226364950e-03
+8.8506488831082628e-02 0.0000000000000000e+00 0.0000000000000000e+00 1.7701297766216512e-03
+9.2118998579290082e-02 0.0000000000000000e+00 0.0000000000000000e+00 1.8423799715858030e-03
+9.5878957704975398e-02 0.0000000000000000e+00 0.0000000000000000e+00 1.9175791540995135e-03
+9.9792384550076441e-02 0.0000000000000000e+00 0.0000000000000000e+00 1.9958476910015288e-03
+1.0386554310314079e-01 0.0000000000000000e+00 0.0000000000000000e+00 2.0773108620628228e-03
diff --git a/orsopy/fileio/base.py b/orsopy/fileio/base.py
@@ -2,12 +2,12 @@
 Implementation of the base classes for the ORSO header.
 """
 
-import sys
 import datetime
 import json
 import os.path
 import pathlib
 import re
+import sys
 import warnings
 
 from collections.abc import Mapping
@@ -39,9 +39,9 @@ def _noop(self, *args, **kw):
 yaml.emitter.Emitter.process_tag = _noop
 
 # make sure that datetime strings get loaded as str not datetime instances
-yaml.constructor.SafeConstructor.yaml_constructors[
-    "tag:yaml.org,2002:timestamp"
-] = yaml.constructor.SafeConstructor.yaml_constructors["tag:yaml.org,2002:str"]
+yaml.constructor.SafeConstructor.yaml_constructors["tag:yaml.org,2002:timestamp"] = (
+    yaml.constructor.SafeConstructor.yaml_constructors["tag:yaml.org,2002:str"]
+)
 
 
 class ORSOResolveError(ValueError):
@@ -284,7 +284,8 @@ def _resolve_type(hint: type, item: Any) -> Any:
                     return item
                 else:
                     warnings.warn(
-                        f"Has to be one of {get_args(hint)} got {item}", ORSOSchemaWarning,
+                        f"Has to be one of {get_args(hint)} got {item}",
+                        ORSOSchemaWarning,
                     )
                     return str(item)
         return None
@@ -424,7 +425,9 @@ def to_nexus(self, root=None, name=None):
                             # special handling for null datasets: no data
                             item_out = child_group.create_dataset(sub_name, dtype="f")
                         elif isinstance(t_value, dict):
-                            item_out = child_group.create_dataset(sub_name, data=json.dumps(t_value))
+                            item_out = child_group.create_dataset(
+                                sub_name, data=json.dumps(t_value, default=lambda o: o.__dict__)
+                            )
                             item_out.attrs["mimetype"] = JSON_MIMETYPE
                         else:
                             # raise ValueError(f"unserializable attribute found: {child_name}[{index}] = {t_value}")
@@ -440,7 +443,7 @@ def to_nexus(self, root=None, name=None):
                 elif t_value is None:
                     group.create_dataset(child_name, dtype="f")
                 elif isinstance(t_value, dict):
-                    dset = group.create_dataset(child_name, data=json.dumps(t_value))
+                    dset = group.create_dataset(child_name, data=json.dumps(t_value, default=lambda o: o.__dict__))
                     dset.attrs["mimetype"] = JSON_MIMETYPE
                 else:
                     warnings.warn(f"unserializable attribute found: {child_name} = {t_value}")
@@ -973,10 +976,7 @@ def _validate_header_data(dct_list: List[dict]):
 
     vi = sys.version_info
     if vi.minor < 7:
-        warnings.warn(
-            "Validation not possible with Python 3.6 with 2020-12 json schema",
-            ORSOSchemaWarning
-        )
+        warnings.warn("Validation not possible with Python 3.6 with 2020-12 json schema", ORSOSchemaWarning)
 
     pth = os.path.dirname(__file__)
     schema_pth = os.path.join(pth, "schema", "refl_header.schema.json")
@@ -1025,7 +1025,7 @@ def _todict(obj: Any, classkey: Any = None) -> dict:
     """
     if isinstance(obj, dict):
         data = {}
-        for (k, v) in obj.items():
+        for k, v in obj.items():
             data[k] = _todict(v, classkey)
         return data
     elif isinstance(obj, Enum):

diff --git a/orsopy/orb2ort.py b/orsopy/orb2ort.py
@@ -0,0 +1,16 @@
+import sys
+
+from .fileio import load_nexus, save_orso
+
+
+def main():
+    for fn in sys.argv[1:]:
+        print(fn)
+        res = load_nexus(fn)
+        save_orso(res, fn.rsplit(".", 1)[0] + ".ort")
+
+
+if __name__ == "__main__":
+    if len(sys.argv) == 1:
+        print("Convert ORSO text representation to Nexus.\nUsage: orsopy.py file1.orb file2.orb ...")
+    main()
diff --git a/orsopy/ort2orb.py b/orsopy/ort2orb.py
@@ -0,0 +1,16 @@
+import sys
+
+from .fileio import load_orso, save_nexus
+
+
+def main():
+    for fn in sys.argv[1:]:
+        print(fn)
+        res = load_orso(fn)
+        save_nexus(res, fn.rsplit(".", 1)[0] + ".orb")
+
+
+if __name__ == "__main__":
+    if len(sys.argv) == 1:
+        print("Convert ORSO text representation to Nexus.\nUsage: orsopy.py file1.ort file2.ort ...")
+    main()