From 66d24f37f40e07e14991db9d9c9aa85a01102dd3 Mon Sep 17 00:00:00 2001
From: Julia Schumann <32182254+schumannj@users.noreply.github.com>
Date: Wed, 29 May 2024 14:49:38 +0000
Subject: [PATCH] fix ir schema
---
normalized_ir.archive.json | 2336 +++++++++++++++++
normalized_nrvs.archive.json | 8 +-
.../schema_packages/mypackage.py | 5 +-
tests/data/ir_test.archive.yaml | 2 +-
4 files changed, 2344 insertions(+), 7 deletions(-)
create mode 100644 normalized_ir.archive.json
diff --git a/normalized_ir.archive.json b/normalized_ir.archive.json
new file mode 100644
index 0000000..1952884
--- /dev/null
+++ b/normalized_ir.archive.json
@@ -0,0 +1,2336 @@
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+ "data_file": "ReRH_Nia-C_H_IR_exp.dat",
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+ "cells": {
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+ "line": {
+ "color": "white"
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+ "header": {
+ "fill": {
+ "color": "#C8D4E3"
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+ "line": {
+ "color": "white"
+ }
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+ "type": "table"
+ }
+ ],
+ "barpolar": [
+ {
+ "marker": {
+ "line": {
+ "color": "#E5ECF6",
+ "width": 0.5
+ },
+ "pattern": {
+ "fillmode": "overlay",
+ "size": 10,
+ "solidity": 0.2
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+ "type": "pie"
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+ "autotypenumbers": "strict",
+ "colorway": [
+ "#636efa",
+ "#EF553B",
+ "#00cc96",
+ "#ab63fa",
+ "#FFA15A",
+ "#19d3f3",
+ "#FF6692",
+ "#B6E880",
+ "#FF97FF",
+ "#FECB52"
+ ],
+ "font": {
+ "color": "#2a3f5f"
+ },
+ "hovermode": "closest",
+ "hoverlabel": {
+ "align": "left"
+ },
+ "paper_bgcolor": "white",
+ "plot_bgcolor": "#E5ECF6",
+ "polar": {
+ "bgcolor": "#E5ECF6",
+ "angularaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "radialaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ }
+ },
+ "ternary": {
+ "bgcolor": "#E5ECF6",
+ "aaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "baxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ },
+ "caxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": ""
+ }
+ },
+ "coloraxis": {
+ "colorbar": {
+ "outlinewidth": 0,
+ "ticks": ""
+ }
+ },
+ "colorscale": {
+ "sequential": [
+ [
+ 0.0,
+ "#0d0887"
+ ],
+ [
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+ "#46039f"
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+ [
+ 0.2222222222222222,
+ "#7201a8"
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+ "#9c179e"
+ ],
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+ "#bd3786"
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+ "#f0f921"
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+ "#0d0887"
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+ "#d8576b"
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+ "#ed7953"
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+ "#fb9f3a"
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+ 0.8888888888888888,
+ "#fdca26"
+ ],
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+ "#f0f921"
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+ [
+ 0,
+ "#8e0152"
+ ],
+ [
+ 0.1,
+ "#c51b7d"
+ ],
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+ 0.2,
+ "#de77ae"
+ ],
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+ 0.3,
+ "#f1b6da"
+ ],
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+ "#fde0ef"
+ ],
+ [
+ 0.5,
+ "#f7f7f7"
+ ],
+ [
+ 0.6,
+ "#e6f5d0"
+ ],
+ [
+ 0.7,
+ "#b8e186"
+ ],
+ [
+ 0.8,
+ "#7fbc41"
+ ],
+ [
+ 0.9,
+ "#4d9221"
+ ],
+ [
+ 1,
+ "#276419"
+ ]
+ ]
+ },
+ "xaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": "",
+ "title": {
+ "standoff": 15
+ },
+ "zerolinecolor": "white",
+ "automargin": true,
+ "zerolinewidth": 2
+ },
+ "yaxis": {
+ "gridcolor": "white",
+ "linecolor": "white",
+ "ticks": "",
+ "title": {
+ "standoff": 15
+ },
+ "zerolinecolor": "white",
+ "automargin": true,
+ "zerolinewidth": 2
+ },
+ "scene": {
+ "xaxis": {
+ "backgroundcolor": "#E5ECF6",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "showbackground": true,
+ "ticks": "",
+ "zerolinecolor": "white",
+ "gridwidth": 2
+ },
+ "yaxis": {
+ "backgroundcolor": "#E5ECF6",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "showbackground": true,
+ "ticks": "",
+ "zerolinecolor": "white",
+ "gridwidth": 2
+ },
+ "zaxis": {
+ "backgroundcolor": "#E5ECF6",
+ "gridcolor": "white",
+ "linecolor": "white",
+ "showbackground": true,
+ "ticks": "",
+ "zerolinecolor": "white",
+ "gridwidth": 2
+ }
+ },
+ "shapedefaults": {
+ "line": {
+ "color": "#2a3f5f"
+ }
+ },
+ "annotationdefaults": {
+ "arrowcolor": "#2a3f5f",
+ "arrowhead": 0,
+ "arrowwidth": 1
+ },
+ "geo": {
+ "bgcolor": "white",
+ "landcolor": "#E5ECF6",
+ "subunitcolor": "white",
+ "showland": true,
+ "showlakes": true,
+ "lakecolor": "white"
+ },
+ "title": {
+ "x": 0.05
+ },
+ "mapbox": {
+ "style": "light"
+ }
+ }
+ },
+ "xaxis": {
+ "anchor": "y",
+ "domain": [
+ 0.0,
+ 1.0
+ ],
+ "title": {
+ "text": "wavenumber, cm-1"
+ }
+ },
+ "yaxis": {
+ "anchor": "x",
+ "domain": [
+ 0.0,
+ 1.0
+ ],
+ "title": {
+ "text": "Absorbance"
+ }
+ },
+ "legend": {
+ "tracegroupgap": 0
+ },
+ "margin": {
+ "t": 60
+ }
+ }
+ }
+ }
+ ]
+ },
+ "workflow2": {
+ "name": "ir test"
+ },
+ "metadata": {
+ "entry_name": "ir_test.archive.yaml",
+ "entry_type": "IRSpectroscopy",
+ "mainfile": "/workspaces/nomad-unisyscat-plugin/tests/data/ir_test.archive.yaml",
+ "text_search_contents": [
+ "IR",
+ "ReRH_Nia-C_H_IR_exp.dat",
+ "ir test"
+ ],
+ "n_quantities": 22,
+ "quantities": [
+ "",
+ "data",
+ "data.data_file",
+ "data.datetime",
+ "data.figures",
+ "data.figures.figure",
+ "data.figures.label",
+ "data.name",
+ "data.results",
+ "data.results.intensity",
+ "data.results.wavenumber",
+ "metadata",
+ "metadata.entry_name",
+ "metadata.entry_type",
+ "metadata.mainfile",
+ "metadata.quantities",
+ "metadata.section_defs",
+ "metadata.section_defs.definition_id",
+ "metadata.section_defs.definition_qualified_name",
+ "metadata.section_defs.used_directly",
+ "metadata.sections",
+ "results",
+ "results.eln",
+ "results.eln.methods",
+ "results.eln.names",
+ "results.eln.sections",
+ "results.properties",
+ "workflow2",
+ "workflow2.name"
+ ],
+ "sections": [
+ "nomad.datamodel.datamodel.EntryArchive",
+ "nomad.datamodel.datamodel.EntryMetadata",
+ "nomad.datamodel.metainfo.plot.PlotlyFigure",
+ "nomad.datamodel.metainfo.workflow.Workflow",
+ "nomad.datamodel.results.ELN",
+ "nomad.datamodel.results.Properties",
+ "nomad.datamodel.results.Results",
+ "nomad_unisyscat.schema_packages.mypackage.IRResult",
+ "nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy"
+ ],
+ "section_defs": [
+ {
+ "definition_qualified_name": "nomad.datamodel.data.ArchiveSection",
+ "definition_id": "7047cbff9980abff17cce4b1b6b0d1c783505b7f",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.data.EntryData",
+ "definition_id": "538f52fd8d52b29372066f878319c6aeb03b74d2",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.datamodel.EntryArchive",
+ "definition_id": "4f8220ef0081f34a08e0cb211ca52e2ee7cc4d1b",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.datamodel.EntryMetadata",
+ "definition_id": "08e24de48352035bcc932ed9934875ed9b10188e",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.basesections.Activity",
+ "definition_id": "fc2735d177bf36f9718ca66a764a56fc0c6200a0",
+ "used_directly": false
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.basesections.ActivityResult",
+ "definition_id": "7a45b4ea57a5d815e77298f59597f9d85fb93499",
+ "used_directly": false
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.basesections.BaseSection",
+ "definition_id": "add2edfa25a61ff3bbfdebacc870181f64f41634",
+ "used_directly": false
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.basesections.Measurement",
+ "definition_id": "92a193e908065fa4ff809fb88e83e3057876be33",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.basesections.MeasurementResult",
+ "definition_id": "b41fee755770982d78a427f10debb30fea469269",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.plot.Figure",
+ "definition_id": "55ef08f33dcf9fb374aea217458bd34a23bec57b",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.plot.PlotSection",
+ "definition_id": "7bb17e35ed91dca88bf6238fc51ed212693593d0",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.plot.PlotlyFigure",
+ "definition_id": "491cdc3c5ea21cdc576275a5c1e600cdaa4256c1",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.workflow.Task",
+ "definition_id": "ac62fdff74f54fd477531446ca111c0dd9df6ba2",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.metainfo.workflow.Workflow",
+ "definition_id": "fc65ae24157492e422afe61173a71403fc5e1fd7",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.results.ELN",
+ "definition_id": "eeed330bd18d40f3a2a00cc35ba6f58808d0c543",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.results.Properties",
+ "definition_id": "f6d62b2664a0c37e0c82d4cb570e5e177e445e05",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad.datamodel.results.Results",
+ "definition_id": "d77c26594ec0501fb0de8daaa4d7b25d54b9e0cf",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad_unisyscat.schema_packages.mypackage.IRResult",
+ "definition_id": "fdf0bb56a72b3d49080686f68bb46715cd2b46dc",
+ "used_directly": true
+ },
+ {
+ "definition_qualified_name": "nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy",
+ "definition_id": "a706f88f552b8fd0ef47841a9fe4db8c6ea3fd33",
+ "used_directly": true
+ }
+ ],
+ "search_quantities": [
+ {
+ "id": "data.data_file#nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy",
+ "definition": "nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy.data_file",
+ "path_archive": "data.data_file",
+ "str_value": "ReRH_Nia-C_H_IR_exp.dat"
+ },
+ {
+ "id": "data.figures.label#nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy",
+ "definition": "nomad.datamodel.metainfo.plot.Figure.label",
+ "path_archive": "data.figures.0.label",
+ "str_value": "IR"
+ },
+ {
+ "id": "data.name#nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy",
+ "definition": "nomad.datamodel.metainfo.basesections.BaseSection.name",
+ "path_archive": "data.name",
+ "str_value": "ir test"
+ },
+ {
+ "id": "data.datetime#nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy",
+ "definition": "nomad.datamodel.metainfo.basesections.Activity.datetime",
+ "path_archive": "data.datetime",
+ "datetime_value": "2024-05-29T14:48:48.377834+00:00"
+ }
+ ]
+ },
+ "results": {
+ "properties": {},
+ "eln": {
+ "sections": [
+ "IRSpectroscopy"
+ ],
+ "names": [
+ "ir test"
+ ],
+ "methods": [
+ "IRSpectroscopy"
+ ]
+ }
+ }
+}
\ No newline at end of file
diff --git a/normalized_nrvs.archive.json b/normalized_nrvs.archive.json
index fa7f411..4e56de8 100644
--- a/normalized_nrvs.archive.json
+++ b/normalized_nrvs.archive.json
@@ -2,7 +2,7 @@
"data": {
"m_def": "nomad_unisyscat.schema_packages.mypackage.NRVSpectroscopy",
"name": "nrvs test",
- "datetime": "2024-05-29T13:52:14.690498+00:00",
+ "datetime": "2024-05-29T14:47:35.680156+00:00",
"measurement_data_file": "ReRH_Nia-C_H_NRVS_exp.dat",
"results": [
{
@@ -2360,9 +2360,9 @@
"entry_type": "NRVSpectroscopy",
"mainfile": "/workspaces/nomad-unisyscat-plugin/tests/data/nrvs_test.archive.yaml",
"text_search_contents": [
+ "ReRH_Nia-C_H_NRVS_exp.dat",
"NRVS",
- "nrvs test",
- "ReRH_Nia-C_H_NRVS_exp.dat"
+ "nrvs test"
],
"n_quantities": 22,
"quantities": [
@@ -2527,7 +2527,7 @@
"id": "data.datetime#nomad_unisyscat.schema_packages.mypackage.NRVSpectroscopy",
"definition": "nomad.datamodel.metainfo.basesections.Activity.datetime",
"path_archive": "data.datetime",
- "datetime_value": "2024-05-29T13:52:14.690498+00:00"
+ "datetime_value": "2024-05-29T14:47:35.680156+00:00"
}
]
},
diff --git a/src/nomad_unisyscat/schema_packages/mypackage.py b/src/nomad_unisyscat/schema_packages/mypackage.py
index 7f87855..aa2374b 100644
--- a/src/nomad_unisyscat/schema_packages/mypackage.py
+++ b/src/nomad_unisyscat/schema_packages/mypackage.py
@@ -116,7 +116,7 @@ def normalize(self, archive, logger):
self.figures = []
- fig = px.line(x=self.results.wavenumber, y=self.results.intensity)
+ fig = px.line(x=data['wavenumber, cm-1'], y=data['57Fe PVDOS'])
fig.update_xaxes(title_text=col_names[0])
fig.update_yaxes(title_text=col_names[1])
self.figures.append(PlotlyFigure(label='NRVS', figure=fig.to_plotly_json()))
@@ -197,6 +197,7 @@ def normalize(self, archive, logger):
col_names = ['wavenumber, cm-1', 'Absorbance']
data = pd.read_csv(f.name, header=None, names=col_names)
+
result = IRResult()
result.wavenumber = data['wavenumber, cm-1']
result.intensity = data['Absorbance']
@@ -206,7 +207,7 @@ def normalize(self, archive, logger):
self.figures = []
- fig = px.line(x=data['wavenumber, cm-1'], y=data['57Fe PVDOS'])
+ fig = px.line(x=data['wavenumber, cm-1'], y=data['Absorbance'])
fig.update_xaxes(title_text=col_names[0])
fig.update_yaxes(title_text=col_names[1])
self.figures.append(PlotlyFigure(label='IR', figure=fig.to_plotly_json()))
diff --git a/tests/data/ir_test.archive.yaml b/tests/data/ir_test.archive.yaml
index cbe87fc..124b331 100644
--- a/tests/data/ir_test.archive.yaml
+++ b/tests/data/ir_test.archive.yaml
@@ -1,3 +1,3 @@
data:
m_def: nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy
- measurement_data_file: ReRH_Nia-C_H_IR_exp.dat
+ data_file: ReRH_Nia-C_H_IR_exp.dat