From 31746372aa8b462160ef3f01b926364722ad6bd6 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Thu, 29 Dec 2022 21:10:18 +0100
Subject: [PATCH 01/11] Adding the new xps_eln.yaml and modify tools.json file
favoring the changes. Also the required changes in Docker-compose.ymal,
Dockerfile and requirement.txt
---
docker/xps/Dockerfile | 4 +-
docker/xps/docker-compose.yml | 5 +-
docker/xps/example/xps_eln.yaml | 47 ++++
docker/xps/requirements.txt | 394 +++++++++++++++++++-------------
tools.json | 8 +-
5 files changed, 295 insertions(+), 163 deletions(-)
create mode 100644 docker/xps/example/xps_eln.yaml
mode change 100755 => 100644 docker/xps/requirements.txt
diff --git a/docker/xps/Dockerfile b/docker/xps/Dockerfile
index 436f59e..e327906 100644
--- a/docker/xps/Dockerfile
+++ b/docker/xps/Dockerfile
@@ -9,5 +9,5 @@ RUN pip install -r requirements.txt \
&& jupyter lab build \
&& jupyter nbextension enable --py widgetsnbextension \
&& jupyter serverextension enable jupyterlab_h5web \
- && pip install git+https://github.com/nomad-coe/nomad-parser-nexus.git@XPS_datamodel_with_cls_AP1
-RUN rm requirements.txt
\ No newline at end of file
+ && pip install git+https://github.com/nomad-coe/nomad-parser-nexus.git@XPS_datamodel_V_new
+RUN rm requirements.txt
diff --git a/docker/xps/docker-compose.yml b/docker/xps/docker-compose.yml
index 53fea18..8700a73 100644
--- a/docker/xps/docker-compose.yml
+++ b/docker/xps/docker-compose.yml
@@ -1,10 +1,11 @@
version: "3.9"
+#image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter
services:
xps:
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter:0.1
ports:
- 8888:8888
volumes:
- ./example:/home/jovyan/work
- working_dir: /home/jovyan/work
\ No newline at end of file
+ working_dir: /home/jovyan/work
diff --git a/docker/xps/example/xps_eln.yaml b/docker/xps/example/xps_eln.yaml
new file mode 100644
index 0000000..bc0ca0e
--- /dev/null
+++ b/docker/xps/example/xps_eln.yaml
@@ -0,0 +1,47 @@
+Instrument:
+ Analyser:
+ Collectioncolumn:
+ scheme: "Angular dispersive"
+ description: "hemispherical"
+ name: null
+ Energydispersion:
+ entrance_slit:
+ scheme: "hemispherical"
+ pass_energy:
+ unit: null
+ Beam:
+ distance:
+ unit: "mm"
+ value: 0.0
+ energy_resolution:
+ unit: null
+ value: null
+ Source:
+ type: "Synchrotron X-ray Source"
+ probe: "x-ray"
+Sample:
+ name: null
+ preparation_description: "From third party"
+ temperature:
+ unit: "K"
+ value: 298.0
+ situation: "vacuum"
+ gas_pressure:
+ unit: "Pa"
+ value: 101325.0
+start_time: null
+definition:
+ version: null
+ value: null
+title: "XPS Experiment"
+start_time: "2022-04-08T11:47:02.0200Z"
+definition:
+ value: "NXmpes"
+ version: 1.0
+User:
+ name: "Ahmed Mansour"
+ email: "amansour@physik.hu-berlin.de"
+Data:
+ BE:
+ unit: null
+
diff --git a/docker/xps/requirements.txt b/docker/xps/requirements.txt
old mode 100755
new mode 100644
index 984f13e..d8015c0
--- a/docker/xps/requirements.txt
+++ b/docker/xps/requirements.txt
@@ -1,25 +1,23 @@
#
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
+# This file is autogenerated by pip-compile with python 3.7
+# To update, run:
#
-# pip-compile
+# pip-compile --output-file=requirements.txt pyproject.toml
#
anyio==3.6.2
# via jupyter-server
argon2-cffi==21.3.0
- # via
- # jupyter-server
- # nbclassic
+ # via jupyter-server
argon2-cffi-bindings==21.2.0
# via argon2-cffi
-asteval==0.9.28
- # via lmfit
-asttokens==2.2.1
- # via stack-data
-attrs==22.1.0
+asciitree==0.3.3
+ # via zarr
+ase==3.22.1
+ # via nexusutils (pyproject.toml)
+astroid==2.12.13
+ # via nexusutils (pyproject.toml)
+attrs==22.2.0
# via jsonschema
-babel==2.11.0
- # via jupyterlab-server
backcall==0.2.0
# via ipython
beautifulsoup4==4.11.1
@@ -29,292 +27,374 @@ bleach==5.0.1
certifi==2022.12.7
# via requests
cffi==1.15.1
- # via
- # argon2-cffi-bindings
- # pynacl
+ # via argon2-cffi-bindings
charset-normalizer==2.1.1
# via requests
-comm==0.1.2
- # via ipykernel
+click==8.1.3
+ # via nexusutils (pyproject.toml)
+cloudpickle==2.2.0
+ # via dask
+cycler==0.11.0
+ # via matplotlib
+dask[array]==2022.2.0
+ # via hyperspy
debugpy==1.6.4
# via ipykernel
decorator==5.1.1
- # via ipython
+ # via
+ # ipyparallel
+ # ipython
defusedxml==0.7.1
# via nbconvert
-deprecated==1.2.13
- # via pygithub
+dill==0.3.6
+ # via hyperspy
entrypoints==0.4
- # via jupyter-client
-executing==1.2.0
- # via stack-data
+ # via
+ # ipyparallel
+ # jupyter-client
+ # numcodecs
+fasteners==0.18
+ # via zarr
fastjsonschema==2.16.2
# via nbformat
-future==0.18.2
- # via uncertainties
-h5glance==0.8
- # via -r requirements.in
-h5grove==1.1.0
+flatdict==4.0.1
+ # via nexusutils (pyproject.toml)
+fonttools==4.38.0
+ # via matplotlib
+fsspec==2022.11.0
# via
- # -r requirements.in
- # jupyterlab-h5web
+ # dask
+ # hyperspy
+future==0.18.2
+ # via h5py-wrapper
+h5grove==1.2.0
+ # via jupyterlab-h5web
h5py==3.7.0
# via
- # h5glance
# h5grove
- # hdf5plugin
- # punx
-hdf5plugin==4.0.1
- # via jupyterlab-h5web
-htmlgen==2.0.0
- # via h5glance
+ # h5py-wrapper
+ # hyperspy
+ # jupyterlab-h5web
+ # nexusutils (pyproject.toml)
+h5py-wrapper==1.1.0
+ # via hdfdict
+hdfdict @ git+https://github.com/shabihsherjeel/hdfdict@f48a586
+ # via nexusutils (pyproject.toml)
+hyperspy==1.7.3
+ # via nexusutils (pyproject.toml)
idna==3.4
# via
# anyio
# requests
-ipykernel==6.19.2
+imageio==2.23.0
+ # via
+ # hyperspy
+ # scikit-image
+importlib-metadata==5.2.0
# via
- # ipywidgets
- # nbclassic
-ipython==8.7.0
+ # click
+ # hyperspy
+ # jsonschema
+ # nbconvert
+ # nbformat
+ # numba
+ # pint
+ # prettytable
+ # xarray
+importlib-resources==5.10.2
+ # via jsonschema
+ipykernel==6.16.2
+ # via ipyparallel
+ipyparallel==8.4.1
+ # via hyperspy
+ipython==7.34.0
# via
+ # hyperspy
# ipykernel
- # ipywidgets
- # jupyterlab
-ipython-genutils==0.2.0
- # via nbclassic
-ipywidgets==8.0.3
- # via -r requirements.in
+ # ipyparallel
jedi==0.18.2
# via ipython
jinja2==3.1.2
# via
+ # hyperspy
# jupyter-server
- # jupyterlab
- # jupyterlab-server
- # nbclassic
# nbconvert
-json5==0.9.10
- # via jupyterlab-server
jsonschema==4.17.3
- # via
- # jupyterlab-server
- # nbformat
+ # via nbformat
jupyter-client==7.4.8
# via
# ipykernel
+ # ipyparallel
# jupyter-server
- # nbclassic
# nbclient
-jupyter-core==5.1.0
+jupyter-core==4.12.0
# via
# jupyter-client
# jupyter-server
- # jupyterlab
- # nbclassic
# nbclient
# nbconvert
# nbformat
-jupyter-server==1.23.3
- # via
- # jupyterlab
- # jupyterlab-h5web
- # jupyterlab-server
- # nbclassic
- # notebook-shim
-jupyterlab[full]==3.2.9
- # via -r requirements.in
-jupyterlab-h5web[full]==6.0.0
- # via -r requirements.in
+jupyter-server==1.23.4
+ # via jupyterlab-h5web
+jupyterlab-h5web==6.5.0
+ # via nexusutils (pyproject.toml)
jupyterlab-pygments==0.2.2
# via nbconvert
-jupyterlab-server==2.16.5
- # via jupyterlab
-jupyterlab-widgets==3.0.4
- # via ipywidgets
-lmfit==1.1.0
- # via -r requirements.in
-lxml==4.9.1
- # via
- # punx
- # pyresttable
+kiwisolver==1.4.4
+ # via matplotlib
+lazy-object-proxy==1.8.0
+ # via astroid
+llvmlite==0.39.1
+ # via numba
+locket==1.0.0
+ # via partd
markupsafe==2.1.1
# via
# jinja2
# nbconvert
+matplotlib==3.5.3
+ # via
+ # ase
+ # hyperspy
matplotlib-inline==0.1.6
# via
# ipykernel
# ipython
mistune==2.0.4
# via nbconvert
-nbclassic==0.4.8
- # via jupyterlab
+mpmath==1.2.1
+ # via sympy
+natsort==8.2.0
+ # via hyperspy
nbclient==0.7.2
# via nbconvert
-nbconvert==7.2.6
- # via
- # jupyter-server
- # nbclassic
-nbformat==5.7.0
+nbconvert==7.2.7
+ # via jupyter-server
+nbformat==5.7.1
# via
# jupyter-server
- # nbclassic
# nbclient
# nbconvert
nest-asyncio==1.5.6
# via
# ipykernel
# jupyter-client
- # nbclassic
-nodejs==0.1.1
- # via -r requirements.in
-notebook-shim==0.2.2
- # via nbclassic
-numpy==1.23.5
+networkx==2.6.3
+ # via scikit-image
+numba==0.56.4
# via
+ # hyperspy
+ # sparse
+numcodecs==0.10.2
+ # via zarr
+numexpr==2.8.4
+ # via hyperspy
+numpy==1.21.6
+ # via
+ # ase
+ # dask
# h5grove
# h5py
- # lmfit
- # punx
- # pyresttable
+ # hyperspy
+ # imageio
+ # matplotlib
+ # nexusutils (pyproject.toml)
+ # numba
+ # numcodecs
+ # numexpr
+ # pandas
+ # pywavelets
+ # scikit-image
# scipy
+ # sparse
# tifffile
-optional-django==0.1.0
- # via nodejs
+ # xarray
+ # zarr
orjson==3.8.3
# via h5grove
packaging==22.0
# via
+ # dask
+ # hyperspy
# ipykernel
# jupyter-server
- # jupyterlab
- # jupyterlab-server
+ # matplotlib
# nbconvert
+ # pint
+ # scikit-image
+pandas==1.3.5
+ # via
+ # nexusutils (pyproject.toml)
+ # xarray
pandocfilters==1.5.0
# via nbconvert
parso==0.8.3
# via jedi
+partd==1.3.0
+ # via dask
pexpect==4.8.0
# via ipython
pickleshare==0.7.5
# via ipython
-platformdirs==2.6.0
- # via jupyter-core
-plotly==5.11.0
- # via -r requirements.in
-prometheus-client==0.15.0
+pillow==9.3.0
# via
- # jupyter-server
- # nbclassic
+ # imageio
+ # matplotlib
+ # scikit-image
+pint==0.18
+ # via hyperspy
+pkgutil-resolve-name==1.3.10
+ # via jsonschema
+prettytable==3.5.0
+ # via hyperspy
+prometheus-client==0.15.0
+ # via jupyter-server
prompt-toolkit==3.0.36
# via ipython
psutil==5.9.4
- # via ipykernel
+ # via
+ # ipykernel
+ # ipyparallel
ptyprocess==0.7.0
# via
# pexpect
# terminado
-punx==0.2.5
- # via -r requirements.in
-pure-eval==0.2.2
- # via stack-data
pycparser==2.21
# via cffi
-pygithub==1.57
- # via punx
pygments==2.13.0
# via
# ipython
# nbconvert
-pyjwt==2.6.0
- # via pygithub
-pynacl==1.5.0
- # via pygithub
-pyresttable==2020.0.6
- # via punx
-pyrsistent==0.19.2
+pyparsing==3.0.9
+ # via matplotlib
+pyrsistent==0.19.3
# via jsonschema
+pytest-runner==6.0.0
+ # via h5py-wrapper
python-dateutil==2.8.2
- # via jupyter-client
-pytz==2022.6
- # via babel
+ # via
+ # hyperspy
+ # ipyparallel
+ # jupyter-client
+ # matplotlib
+ # pandas
+pytz==2022.7
+ # via
+ # nexusutils (pyproject.toml)
+ # pandas
+pywavelets==1.3.0
+ # via scikit-image
+pyyaml==6.0
+ # via
+ # dask
+ # hdfdict
+ # hyperspy
+ # nexusutils (pyproject.toml)
pyzmq==24.0.1
# via
# ipykernel
+ # ipyparallel
# jupyter-client
# jupyter-server
- # nbclassic
requests==2.28.1
+ # via hyperspy
+scikit-image==0.19.3
+ # via hyperspy
+scipy==1.7.3
# via
- # jupyterlab-server
- # punx
- # pygithub
-scipy==1.9.3
- # via lmfit
+ # ase
+ # hyperspy
+ # scikit-image
+ # sparse
send2trash==1.8.0
- # via
- # jupyter-server
- # nbclassic
+ # via jupyter-server
six==1.16.0
# via
- # asttokens
# bleach
# python-dateutil
sniffio==1.3.0
# via anyio
soupsieve==2.3.2.post1
# via beautifulsoup4
-stack-data==0.6.2
- # via ipython
-tenacity==8.1.0
- # via plotly
+sparse==0.13.0
+ # via hyperspy
+sympy==1.10.1
+ # via hyperspy
terminado==0.17.1
+ # via jupyter-server
+tifffile==2021.11.2
# via
- # jupyter-server
- # nbclassic
-tifffile==2022.10.10
- # via h5grove
+ # h5grove
+ # hyperspy
+ # scikit-image
tinycss2==1.2.1
# via nbconvert
+toolz==0.12.0
+ # via
+ # dask
+ # hyperspy
+ # partd
tornado==6.2
# via
# ipykernel
+ # ipyparallel
# jupyter-client
# jupyter-server
- # jupyterlab
- # nbclassic
# terminado
-traitlets==5.7.1
+tqdm==4.64.1
+ # via
+ # hyperspy
+ # ipyparallel
+traitlets==5.8.0
# via
- # comm
# ipykernel
+ # ipyparallel
# ipython
- # ipywidgets
# jupyter-client
# jupyter-core
# jupyter-server
# matplotlib-inline
- # nbclassic
# nbclient
# nbconvert
# nbformat
-uncertainties==3.1.7
- # via lmfit
+traits==6.4.1
+ # via hyperspy
+typed-ast==1.5.4
+ # via
+ # astroid
+ # nexusutils (pyproject.toml)
+typing-extensions==4.4.0
+ # via
+ # anyio
+ # argon2-cffi
+ # astroid
+ # importlib-metadata
+ # jsonschema
+ # kiwisolver
+ # numcodecs
+ # xarray
urllib3==1.26.13
# via requests
wcwidth==0.2.5
- # via prompt-toolkit
+ # via
+ # prettytable
+ # prompt-toolkit
webencodings==0.5.1
# via
# bleach
# tinycss2
websocket-client==1.4.2
# via jupyter-server
-widgetsnbextension==4.0.4
- # via ipywidgets
wrapt==1.14.1
- # via deprecated
+ # via astroid
+xarray==0.20.2
+ # via nexusutils (pyproject.toml)
+zarr==2.12.0
+ # via hyperspy
+zipp==3.11.0
+ # via
+ # importlib-metadata
+ # importlib-resources
# The following packages are considered to be unsafe in a requirements file:
-# pip
+# setuptools
diff --git a/tools.json b/tools.json
index 0aec6b8..e73f378 100644
--- a/tools.json
+++ b/tools.json
@@ -96,7 +96,7 @@
"xps": {
"short_description": "An example for analyzing XPS data.",
"description": "Includes tools for analyzing XPS spectra and converting SPECS xml files into NeXus.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter:0.1",
"mount_path": "/home/jovyan",
"file_extensions": [
"ipynb",
@@ -108,6 +108,10 @@
{
"name": "Florian Dobener",
"email": "florian.dobener@physik.hu-berlin.de"
+ },
+ {
+ "name": "Rubel Mozumder",
+ "email": "rubel.mozumder@physik.hu-berlin.de"
}
]
},
@@ -174,4 +178,4 @@
}
]
}
-}
\ No newline at end of file
+}
--
GitLab
From 6b24334f74c570f7fd4028a8dd1e1b7a49763eeb Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Fri, 30 Dec 2022 16:02:40 +0100
Subject: [PATCH 02/11] eln_data: Renaming xps_eln.yaml to eln_data.yaml
---
docker/xps/example/eln_data.yaml | 47 ++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
create mode 100644 docker/xps/example/eln_data.yaml
diff --git a/docker/xps/example/eln_data.yaml b/docker/xps/example/eln_data.yaml
new file mode 100644
index 0000000..bc0ca0e
--- /dev/null
+++ b/docker/xps/example/eln_data.yaml
@@ -0,0 +1,47 @@
+Instrument:
+ Analyser:
+ Collectioncolumn:
+ scheme: "Angular dispersive"
+ description: "hemispherical"
+ name: null
+ Energydispersion:
+ entrance_slit:
+ scheme: "hemispherical"
+ pass_energy:
+ unit: null
+ Beam:
+ distance:
+ unit: "mm"
+ value: 0.0
+ energy_resolution:
+ unit: null
+ value: null
+ Source:
+ type: "Synchrotron X-ray Source"
+ probe: "x-ray"
+Sample:
+ name: null
+ preparation_description: "From third party"
+ temperature:
+ unit: "K"
+ value: 298.0
+ situation: "vacuum"
+ gas_pressure:
+ unit: "Pa"
+ value: 101325.0
+start_time: null
+definition:
+ version: null
+ value: null
+title: "XPS Experiment"
+start_time: "2022-04-08T11:47:02.0200Z"
+definition:
+ value: "NXmpes"
+ version: 1.0
+User:
+ name: "Ahmed Mansour"
+ email: "amansour@physik.hu-berlin.de"
+Data:
+ BE:
+ unit: null
+
--
GitLab
From 6b45324d92114ae6eba83f8a187b688ee90dd72e Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 12:12:05 +0100
Subject: [PATCH 03/11] XPS example modifying file and add path_prefix and icon
elent
---
docker/xps/example/xps_eln.yaml | 47 ---------------------------------
tools.json | 6 +++--
2 files changed, 4 insertions(+), 49 deletions(-)
delete mode 100644 docker/xps/example/xps_eln.yaml
diff --git a/docker/xps/example/xps_eln.yaml b/docker/xps/example/xps_eln.yaml
deleted file mode 100644
index bc0ca0e..0000000
--- a/docker/xps/example/xps_eln.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-Instrument:
- Analyser:
- Collectioncolumn:
- scheme: "Angular dispersive"
- description: "hemispherical"
- name: null
- Energydispersion:
- entrance_slit:
- scheme: "hemispherical"
- pass_energy:
- unit: null
- Beam:
- distance:
- unit: "mm"
- value: 0.0
- energy_resolution:
- unit: null
- value: null
- Source:
- type: "Synchrotron X-ray Source"
- probe: "x-ray"
-Sample:
- name: null
- preparation_description: "From third party"
- temperature:
- unit: "K"
- value: 298.0
- situation: "vacuum"
- gas_pressure:
- unit: "Pa"
- value: 101325.0
-start_time: null
-definition:
- version: null
- value: null
-title: "XPS Experiment"
-start_time: "2022-04-08T11:47:02.0200Z"
-definition:
- value: "NXmpes"
- version: 1.0
-User:
- name: "Ahmed Mansour"
- email: "amansour@physik.hu-berlin.de"
-Data:
- BE:
- unit: null
-
diff --git a/tools.json b/tools.json
index e73f378..8780b98 100644
--- a/tools.json
+++ b/tools.json
@@ -95,9 +95,11 @@
},
"xps": {
"short_description": "An example for analyzing XPS data.",
- "description": "Includes tools for analyzing XPS spectra and converting SPECS xml files into NeXus.",
+ "description": "Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS xml files into NeXus.",
"image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter:0.1",
- "mount_path": "/home/jovyan",
+ "path_prefix": "lab",
+ "icon": "jupyter_logo.svg",
+ "mount_path": "/home/jovyan",
"file_extensions": [
"ipynb",
"nxs",
--
GitLab
From bd20d95224b17c747c14f1ab8fff8a3252eedd4c Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 16:18:05 +0100
Subject: [PATCH 04/11] Imcluding update from
'docker/webtop/north-guacamole-client'
---
docker/webtop/north-guacamole-client | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docker/webtop/north-guacamole-client b/docker/webtop/north-guacamole-client
index 5db00ee..b965bc7 160000
--- a/docker/webtop/north-guacamole-client
+++ b/docker/webtop/north-guacamole-client
@@ -1 +1 @@
-Subproject commit 5db00ee2e62ccf1bde11ed7c82fe8eedd609537f
+Subproject commit b965bc735ab48ce7c21676e616b32d3fa8fd69fc
--
GitLab
From b2db2a9f1965af4c3d5fea1d287395d5d7e75801 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 17:54:01 +0100
Subject: [PATCH 05/11] Update eln_data and config.
---
docker/xps/example/config_file.json | 55 +++++++++++++++++++++--------
docker/xps/example/eln_data.yaml | 6 +++-
2 files changed, 45 insertions(+), 16 deletions(-)
diff --git a/docker/xps/example/config_file.json b/docker/xps/example/config_file.json
index 2756b2b..155cfda 100644
--- a/docker/xps/example/config_file.json
+++ b/docker/xps/example/config_file.json
@@ -1,17 +1,42 @@
+
{
- "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/description": "hemispherical",
- "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]/scheme": "Angular dispersive",
- "/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance": "0.0",
- "/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance/@units": "mm",
- "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/type": "Synchrotron X-ray Source",
- "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/probe": "x-ray",
- "/ENTRY[entry]/SAMPLE[sample]/preparation_description": "Sample comes from third party",
- "/ENTRY[entry]/SAMPLE[sample]/temperature": "298",
- "/ENTRY[entry]/SAMPLE[sample]/temperature/@units": "K",
- "/ENTRY[entry]/SAMPLE[sample]/situation": "vacuum",
- "/ENTRY[entry]/SAMPLE[sample]/gas_pressure": "101325",
- "/ENTRY[entry]/SAMPLE[sample]/gas_pressure/@units": "Pa",
- "/ENTRY[entry]/start_time": "2022-04-08T11:47:02.0200Z",
- "/ENTRY[entry]/USER[user]/name": "Ahmed Mansour",
- "/ENTRY[entry]/USER[user]/email": "amansour@physik.hu-berlin.de"
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/description": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/name": "@xps_tocken:analyzer_info/name",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/entrance_slit": "@xps_tocken:region/analyzer_slit",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/scheme": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/pass_energy": "@xps_tocken:region/pass_energy",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/pass_energy/@units": "eV",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/energy_scan_mode": "@xps_tocken:region/scan_mode/name",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/DATA[data]/raw": "@detector_data:cycles/Cycle_",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/DATA[data]/raw/@units": "counts",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/amplifier_type": "channeltron",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/detector_type": "multi-anode",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]/scheme": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance/@units": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/incident_energy": "@xps_tocken:region/excitation_energy",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/incident_energy/@units": "eV",
+"/ENTRY[entry]/INSTRUMENT[instrument]/energy_resolution": "@xps_tocken:region/scan_delta",
+"/ENTRY[entry]/INSTRUMENT[instrument]/energy_resolution/@units": "eV",
+"/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/type": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/name": "@xps_tocken:source_info/name",
+"/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/probe": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/name": "@xps_tocken:parameters/Group",
+"/ENTRY[entry]/SAMPLE[sample]/preparation_description": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/temperature": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/temperature/@units": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/situation": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/gas_pressure": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/gas_pressure/@units": "@eln",
+"/ENTRY[entry]/DATA[data]/@signal": "",
+"/ENTRY[entry]/DATA[data]/data": "@data:cycles/Cycle_",
+"/ENTRY[entry]/DATA[data]/data/@units": "counts",
+"/ENTRY[entry]/DATA[data]/EB": "counts",
+"/ENTRY[entry]/DATA[data]/EB/@units": "eV",
+"/ENTRY[entry]/title": "@eln",
+"/ENTRY[entry]/start_time": "@eln",
+"/ENTRY[entry]/definition": "@eln",
+"/ENTRY[entry]/definition/@version": "@eln",
+"/ENTRY[entry]/USER[user]/name": "@eln",
+"/ENTRY[entry]/USER[user]/email": "@eln"
}
\ No newline at end of file
diff --git a/docker/xps/example/eln_data.yaml b/docker/xps/example/eln_data.yaml
index bc0ca0e..923bf97 100644
--- a/docker/xps/example/eln_data.yaml
+++ b/docker/xps/example/eln_data.yaml
@@ -2,13 +2,17 @@ Instrument:
Analyser:
Collectioncolumn:
scheme: "Angular dispersive"
+ mode: "Unknown"
description: "hemispherical"
name: null
Energydispersion:
- entrance_slit:
+ entrance_slit: "Unknown"
scheme: "hemispherical"
pass_energy:
unit: null
+ Detector:
+ amplifier_type: "channeltron"
+ detector_type: "Multi-anode"
Beam:
distance:
unit: "mm"
--
GitLab
From 9f6ed5f476630cee5cae57ea7def1fc9be646942 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 22:08:43 +0100
Subject: [PATCH 06/11] Removing path prefix
---
tools.json | 1 -
1 file changed, 1 deletion(-)
diff --git a/tools.json b/tools.json
index 8780b98..c31c06d 100644
--- a/tools.json
+++ b/tools.json
@@ -97,7 +97,6 @@
"short_description": "An example for analyzing XPS data.",
"description": "Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS xml files into NeXus.",
"image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter:0.1",
- "path_prefix": "lab",
"icon": "jupyter_logo.svg",
"mount_path": "/home/jovyan",
"file_extensions": [
--
GitLab
From 090f06f23fdb632c6f44e5a7bfb1e173c23199fe Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Thu, 29 Dec 2022 21:10:18 +0100
Subject: [PATCH 07/11] Adding the new xps_eln.yaml and modify tools.json file
favoring the changes. Also the required changes in Docker-compose.ymal,
Dockerfile and requirement.txt
---
docker/webtop/north-guacamole-client | 2 +-
docker/xps/Dockerfile | 4 +-
docker/xps/docker-compose.yml | 5 +-
docker/xps/example/xps_eln.yaml | 47 ++++
docker/xps/requirements.txt | 394 ++++++++++++++++-----------
tools.json | 6 +-
6 files changed, 295 insertions(+), 163 deletions(-)
create mode 100644 docker/xps/example/xps_eln.yaml
mode change 100755 => 100644 docker/xps/requirements.txt
diff --git a/docker/webtop/north-guacamole-client b/docker/webtop/north-guacamole-client
index 5db00ee..b965bc7 160000
--- a/docker/webtop/north-guacamole-client
+++ b/docker/webtop/north-guacamole-client
@@ -1 +1 @@
-Subproject commit 5db00ee2e62ccf1bde11ed7c82fe8eedd609537f
+Subproject commit b965bc735ab48ce7c21676e616b32d3fa8fd69fc
diff --git a/docker/xps/Dockerfile b/docker/xps/Dockerfile
index 436f59e..e327906 100644
--- a/docker/xps/Dockerfile
+++ b/docker/xps/Dockerfile
@@ -9,5 +9,5 @@ RUN pip install -r requirements.txt \
&& jupyter lab build \
&& jupyter nbextension enable --py widgetsnbextension \
&& jupyter serverextension enable jupyterlab_h5web \
- && pip install git+https://github.com/nomad-coe/nomad-parser-nexus.git@XPS_datamodel_with_cls_AP1
-RUN rm requirements.txt
\ No newline at end of file
+ && pip install git+https://github.com/nomad-coe/nomad-parser-nexus.git@XPS_datamodel_V_new
+RUN rm requirements.txt
diff --git a/docker/xps/docker-compose.yml b/docker/xps/docker-compose.yml
index 53fea18..8700a73 100644
--- a/docker/xps/docker-compose.yml
+++ b/docker/xps/docker-compose.yml
@@ -1,10 +1,11 @@
version: "3.9"
+#image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter
services:
xps:
- image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter
+ image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter:0.1
ports:
- 8888:8888
volumes:
- ./example:/home/jovyan/work
- working_dir: /home/jovyan/work
\ No newline at end of file
+ working_dir: /home/jovyan/work
diff --git a/docker/xps/example/xps_eln.yaml b/docker/xps/example/xps_eln.yaml
new file mode 100644
index 0000000..bc0ca0e
--- /dev/null
+++ b/docker/xps/example/xps_eln.yaml
@@ -0,0 +1,47 @@
+Instrument:
+ Analyser:
+ Collectioncolumn:
+ scheme: "Angular dispersive"
+ description: "hemispherical"
+ name: null
+ Energydispersion:
+ entrance_slit:
+ scheme: "hemispherical"
+ pass_energy:
+ unit: null
+ Beam:
+ distance:
+ unit: "mm"
+ value: 0.0
+ energy_resolution:
+ unit: null
+ value: null
+ Source:
+ type: "Synchrotron X-ray Source"
+ probe: "x-ray"
+Sample:
+ name: null
+ preparation_description: "From third party"
+ temperature:
+ unit: "K"
+ value: 298.0
+ situation: "vacuum"
+ gas_pressure:
+ unit: "Pa"
+ value: 101325.0
+start_time: null
+definition:
+ version: null
+ value: null
+title: "XPS Experiment"
+start_time: "2022-04-08T11:47:02.0200Z"
+definition:
+ value: "NXmpes"
+ version: 1.0
+User:
+ name: "Ahmed Mansour"
+ email: "amansour@physik.hu-berlin.de"
+Data:
+ BE:
+ unit: null
+
diff --git a/docker/xps/requirements.txt b/docker/xps/requirements.txt
old mode 100755
new mode 100644
index 984f13e..d8015c0
--- a/docker/xps/requirements.txt
+++ b/docker/xps/requirements.txt
@@ -1,25 +1,23 @@
#
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
+# This file is autogenerated by pip-compile with python 3.7
+# To update, run:
#
-# pip-compile
+# pip-compile --output-file=requirements.txt pyproject.toml
#
anyio==3.6.2
# via jupyter-server
argon2-cffi==21.3.0
- # via
- # jupyter-server
- # nbclassic
+ # via jupyter-server
argon2-cffi-bindings==21.2.0
# via argon2-cffi
-asteval==0.9.28
- # via lmfit
-asttokens==2.2.1
- # via stack-data
-attrs==22.1.0
+asciitree==0.3.3
+ # via zarr
+ase==3.22.1
+ # via nexusutils (pyproject.toml)
+astroid==2.12.13
+ # via nexusutils (pyproject.toml)
+attrs==22.2.0
# via jsonschema
-babel==2.11.0
- # via jupyterlab-server
backcall==0.2.0
# via ipython
beautifulsoup4==4.11.1
@@ -29,292 +27,374 @@ bleach==5.0.1
certifi==2022.12.7
# via requests
cffi==1.15.1
- # via
- # argon2-cffi-bindings
- # pynacl
+ # via argon2-cffi-bindings
charset-normalizer==2.1.1
# via requests
-comm==0.1.2
- # via ipykernel
+click==8.1.3
+ # via nexusutils (pyproject.toml)
+cloudpickle==2.2.0
+ # via dask
+cycler==0.11.0
+ # via matplotlib
+dask[array]==2022.2.0
+ # via hyperspy
debugpy==1.6.4
# via ipykernel
decorator==5.1.1
- # via ipython
+ # via
+ # ipyparallel
+ # ipython
defusedxml==0.7.1
# via nbconvert
-deprecated==1.2.13
- # via pygithub
+dill==0.3.6
+ # via hyperspy
entrypoints==0.4
- # via jupyter-client
-executing==1.2.0
- # via stack-data
+ # via
+ # ipyparallel
+ # jupyter-client
+ # numcodecs
+fasteners==0.18
+ # via zarr
fastjsonschema==2.16.2
# via nbformat
-future==0.18.2
- # via uncertainties
-h5glance==0.8
- # via -r requirements.in
-h5grove==1.1.0
+flatdict==4.0.1
+ # via nexusutils (pyproject.toml)
+fonttools==4.38.0
+ # via matplotlib
+fsspec==2022.11.0
# via
- # -r requirements.in
- # jupyterlab-h5web
+ # dask
+ # hyperspy
+future==0.18.2
+ # via h5py-wrapper
+h5grove==1.2.0
+ # via jupyterlab-h5web
h5py==3.7.0
# via
- # h5glance
# h5grove
- # hdf5plugin
- # punx
-hdf5plugin==4.0.1
- # via jupyterlab-h5web
-htmlgen==2.0.0
- # via h5glance
+ # h5py-wrapper
+ # hyperspy
+ # jupyterlab-h5web
+ # nexusutils (pyproject.toml)
+h5py-wrapper==1.1.0
+ # via hdfdict
+hdfdict @ git+https://github.com/shabihsherjeel/hdfdict@f48a586
+ # via nexusutils (pyproject.toml)
+hyperspy==1.7.3
+ # via nexusutils (pyproject.toml)
idna==3.4
# via
# anyio
# requests
-ipykernel==6.19.2
+imageio==2.23.0
+ # via
+ # hyperspy
+ # scikit-image
+importlib-metadata==5.2.0
# via
- # ipywidgets
- # nbclassic
-ipython==8.7.0
+ # click
+ # hyperspy
+ # jsonschema
+ # nbconvert
+ # nbformat
+ # numba
+ # pint
+ # prettytable
+ # xarray
+importlib-resources==5.10.2
+ # via jsonschema
+ipykernel==6.16.2
+ # via ipyparallel
+ipyparallel==8.4.1
+ # via hyperspy
+ipython==7.34.0
# via
+ # hyperspy
# ipykernel
- # ipywidgets
- # jupyterlab
-ipython-genutils==0.2.0
- # via nbclassic
-ipywidgets==8.0.3
- # via -r requirements.in
+ # ipyparallel
jedi==0.18.2
# via ipython
jinja2==3.1.2
# via
+ # hyperspy
# jupyter-server
- # jupyterlab
- # jupyterlab-server
- # nbclassic
# nbconvert
-json5==0.9.10
- # via jupyterlab-server
jsonschema==4.17.3
- # via
- # jupyterlab-server
- # nbformat
+ # via nbformat
jupyter-client==7.4.8
# via
# ipykernel
+ # ipyparallel
# jupyter-server
- # nbclassic
# nbclient
-jupyter-core==5.1.0
+jupyter-core==4.12.0
# via
# jupyter-client
# jupyter-server
- # jupyterlab
- # nbclassic
# nbclient
# nbconvert
# nbformat
-jupyter-server==1.23.3
- # via
- # jupyterlab
- # jupyterlab-h5web
- # jupyterlab-server
- # nbclassic
- # notebook-shim
-jupyterlab[full]==3.2.9
- # via -r requirements.in
-jupyterlab-h5web[full]==6.0.0
- # via -r requirements.in
+jupyter-server==1.23.4
+ # via jupyterlab-h5web
+jupyterlab-h5web==6.5.0
+ # via nexusutils (pyproject.toml)
jupyterlab-pygments==0.2.2
# via nbconvert
-jupyterlab-server==2.16.5
- # via jupyterlab
-jupyterlab-widgets==3.0.4
- # via ipywidgets
-lmfit==1.1.0
- # via -r requirements.in
-lxml==4.9.1
- # via
- # punx
- # pyresttable
+kiwisolver==1.4.4
+ # via matplotlib
+lazy-object-proxy==1.8.0
+ # via astroid
+llvmlite==0.39.1
+ # via numba
+locket==1.0.0
+ # via partd
markupsafe==2.1.1
# via
# jinja2
# nbconvert
+matplotlib==3.5.3
+ # via
+ # ase
+ # hyperspy
matplotlib-inline==0.1.6
# via
# ipykernel
# ipython
mistune==2.0.4
# via nbconvert
-nbclassic==0.4.8
- # via jupyterlab
+mpmath==1.2.1
+ # via sympy
+natsort==8.2.0
+ # via hyperspy
nbclient==0.7.2
# via nbconvert
-nbconvert==7.2.6
- # via
- # jupyter-server
- # nbclassic
-nbformat==5.7.0
+nbconvert==7.2.7
+ # via jupyter-server
+nbformat==5.7.1
# via
# jupyter-server
- # nbclassic
# nbclient
# nbconvert
nest-asyncio==1.5.6
# via
# ipykernel
# jupyter-client
- # nbclassic
-nodejs==0.1.1
- # via -r requirements.in
-notebook-shim==0.2.2
- # via nbclassic
-numpy==1.23.5
+networkx==2.6.3
+ # via scikit-image
+numba==0.56.4
# via
+ # hyperspy
+ # sparse
+numcodecs==0.10.2
+ # via zarr
+numexpr==2.8.4
+ # via hyperspy
+numpy==1.21.6
+ # via
+ # ase
+ # dask
# h5grove
# h5py
- # lmfit
- # punx
- # pyresttable
+ # hyperspy
+ # imageio
+ # matplotlib
+ # nexusutils (pyproject.toml)
+ # numba
+ # numcodecs
+ # numexpr
+ # pandas
+ # pywavelets
+ # scikit-image
# scipy
+ # sparse
# tifffile
-optional-django==0.1.0
- # via nodejs
+ # xarray
+ # zarr
orjson==3.8.3
# via h5grove
packaging==22.0
# via
+ # dask
+ # hyperspy
# ipykernel
# jupyter-server
- # jupyterlab
- # jupyterlab-server
+ # matplotlib
# nbconvert
+ # pint
+ # scikit-image
+pandas==1.3.5
+ # via
+ # nexusutils (pyproject.toml)
+ # xarray
pandocfilters==1.5.0
# via nbconvert
parso==0.8.3
# via jedi
+partd==1.3.0
+ # via dask
pexpect==4.8.0
# via ipython
pickleshare==0.7.5
# via ipython
-platformdirs==2.6.0
- # via jupyter-core
-plotly==5.11.0
- # via -r requirements.in
-prometheus-client==0.15.0
+pillow==9.3.0
# via
- # jupyter-server
- # nbclassic
+ # imageio
+ # matplotlib
+ # scikit-image
+pint==0.18
+ # via hyperspy
+pkgutil-resolve-name==1.3.10
+ # via jsonschema
+prettytable==3.5.0
+ # via hyperspy
+prometheus-client==0.15.0
+ # via jupyter-server
prompt-toolkit==3.0.36
# via ipython
psutil==5.9.4
- # via ipykernel
+ # via
+ # ipykernel
+ # ipyparallel
ptyprocess==0.7.0
# via
# pexpect
# terminado
-punx==0.2.5
- # via -r requirements.in
-pure-eval==0.2.2
- # via stack-data
pycparser==2.21
# via cffi
-pygithub==1.57
- # via punx
pygments==2.13.0
# via
# ipython
# nbconvert
-pyjwt==2.6.0
- # via pygithub
-pynacl==1.5.0
- # via pygithub
-pyresttable==2020.0.6
- # via punx
-pyrsistent==0.19.2
+pyparsing==3.0.9
+ # via matplotlib
+pyrsistent==0.19.3
# via jsonschema
+pytest-runner==6.0.0
+ # via h5py-wrapper
python-dateutil==2.8.2
- # via jupyter-client
-pytz==2022.6
- # via babel
+ # via
+ # hyperspy
+ # ipyparallel
+ # jupyter-client
+ # matplotlib
+ # pandas
+pytz==2022.7
+ # via
+ # nexusutils (pyproject.toml)
+ # pandas
+pywavelets==1.3.0
+ # via scikit-image
+pyyaml==6.0
+ # via
+ # dask
+ # hdfdict
+ # hyperspy
+ # nexusutils (pyproject.toml)
pyzmq==24.0.1
# via
# ipykernel
+ # ipyparallel
# jupyter-client
# jupyter-server
- # nbclassic
requests==2.28.1
+ # via hyperspy
+scikit-image==0.19.3
+ # via hyperspy
+scipy==1.7.3
# via
- # jupyterlab-server
- # punx
- # pygithub
-scipy==1.9.3
- # via lmfit
+ # ase
+ # hyperspy
+ # scikit-image
+ # sparse
send2trash==1.8.0
- # via
- # jupyter-server
- # nbclassic
+ # via jupyter-server
six==1.16.0
# via
- # asttokens
# bleach
# python-dateutil
sniffio==1.3.0
# via anyio
soupsieve==2.3.2.post1
# via beautifulsoup4
-stack-data==0.6.2
- # via ipython
-tenacity==8.1.0
- # via plotly
+sparse==0.13.0
+ # via hyperspy
+sympy==1.10.1
+ # via hyperspy
terminado==0.17.1
+ # via jupyter-server
+tifffile==2021.11.2
# via
- # jupyter-server
- # nbclassic
-tifffile==2022.10.10
- # via h5grove
+ # h5grove
+ # hyperspy
+ # scikit-image
tinycss2==1.2.1
# via nbconvert
+toolz==0.12.0
+ # via
+ # dask
+ # hyperspy
+ # partd
tornado==6.2
# via
# ipykernel
+ # ipyparallel
# jupyter-client
# jupyter-server
- # jupyterlab
- # nbclassic
# terminado
-traitlets==5.7.1
+tqdm==4.64.1
+ # via
+ # hyperspy
+ # ipyparallel
+traitlets==5.8.0
# via
- # comm
# ipykernel
+ # ipyparallel
# ipython
- # ipywidgets
# jupyter-client
# jupyter-core
# jupyter-server
# matplotlib-inline
- # nbclassic
# nbclient
# nbconvert
# nbformat
-uncertainties==3.1.7
- # via lmfit
+traits==6.4.1
+ # via hyperspy
+typed-ast==1.5.4
+ # via
+ # astroid
+ # nexusutils (pyproject.toml)
+typing-extensions==4.4.0
+ # via
+ # anyio
+ # argon2-cffi
+ # astroid
+ # importlib-metadata
+ # jsonschema
+ # kiwisolver
+ # numcodecs
+ # xarray
urllib3==1.26.13
# via requests
wcwidth==0.2.5
- # via prompt-toolkit
+ # via
+ # prettytable
+ # prompt-toolkit
webencodings==0.5.1
# via
# bleach
# tinycss2
websocket-client==1.4.2
# via jupyter-server
-widgetsnbextension==4.0.4
- # via ipywidgets
wrapt==1.14.1
- # via deprecated
+ # via astroid
+xarray==0.20.2
+ # via nexusutils (pyproject.toml)
+zarr==2.12.0
+ # via hyperspy
+zipp==3.11.0
+ # via
+ # importlib-metadata
+ # importlib-resources
# The following packages are considered to be unsafe in a requirements file:
-# pip
+# setuptools
diff --git a/tools.json b/tools.json
index afc7f50..98d2a16 100644
--- a/tools.json
+++ b/tools.json
@@ -110,6 +110,10 @@
{
"name": "Florian Dobener",
"email": "florian.dobener@physik.hu-berlin.de"
+ },
+ {
+ "name": "Rubel Mozumder",
+ "email": "rubel.mozumder@physik.hu-berlin.de"
}
]
},
@@ -176,4 +180,4 @@
}
]
}
-}
\ No newline at end of file
+}
--
GitLab
From f02f07c556858ed75ff5d5c4779d1a5153cade36 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Fri, 30 Dec 2022 16:02:40 +0100
Subject: [PATCH 08/11] eln_data: Renaming xps_eln.yaml to eln_data.yaml
---
docker/xps/example/eln_data.yaml | 47 ++++++++++++++++++++++++++++++++
1 file changed, 47 insertions(+)
create mode 100644 docker/xps/example/eln_data.yaml
diff --git a/docker/xps/example/eln_data.yaml b/docker/xps/example/eln_data.yaml
new file mode 100644
index 0000000..bc0ca0e
--- /dev/null
+++ b/docker/xps/example/eln_data.yaml
@@ -0,0 +1,47 @@
+Instrument:
+ Analyser:
+ Collectioncolumn:
+ scheme: "Angular dispersive"
+ description: "hemispherical"
+ name: null
+ Energydispersion:
+ entrance_slit:
+ scheme: "hemispherical"
+ pass_energy:
+ unit: null
+ Beam:
+ distance:
+ unit: "mm"
+ value: 0.0
+ energy_resolution:
+ unit: null
+ value: null
+ Source:
+ type: "Synchrotron X-ray Source"
+ probe: "x-ray"
+Sample:
+ name: null
+ preparation_description: "From third party"
+ temperature:
+ unit: "K"
+ value: 298.0
+ situation: "vacuum"
+ gas_pressure:
+ unit: "Pa"
+ value: 101325.0
+start_time: null
+definition:
+ version: null
+ value: null
+title: "XPS Experiment"
+start_time: "2022-04-08T11:47:02.0200Z"
+definition:
+ value: "NXmpes"
+ version: 1.0
+User:
+ name: "Ahmed Mansour"
+ email: "amansour@physik.hu-berlin.de"
+Data:
+ BE:
+ unit: null
+
--
GitLab
From 57edac2f823c2d04b9c18313bdfead3e6d4ea860 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 12:12:05 +0100
Subject: [PATCH 09/11] XPS example modifying file and add path_prefix and icon
elent
---
docker/xps/example/xps_eln.yaml | 47 ---------------------------------
1 file changed, 47 deletions(-)
delete mode 100644 docker/xps/example/xps_eln.yaml
diff --git a/docker/xps/example/xps_eln.yaml b/docker/xps/example/xps_eln.yaml
deleted file mode 100644
index bc0ca0e..0000000
--- a/docker/xps/example/xps_eln.yaml
+++ /dev/null
@@ -1,47 +0,0 @@
-Instrument:
- Analyser:
- Collectioncolumn:
- scheme: "Angular dispersive"
- description: "hemispherical"
- name: null
- Energydispersion:
- entrance_slit:
- scheme: "hemispherical"
- pass_energy:
- unit: null
- Beam:
- distance:
- unit: "mm"
- value: 0.0
- energy_resolution:
- unit: null
- value: null
- Source:
- type: "Synchrotron X-ray Source"
- probe: "x-ray"
-Sample:
- name: null
- preparation_description: "From third party"
- temperature:
- unit: "K"
- value: 298.0
- situation: "vacuum"
- gas_pressure:
- unit: "Pa"
- value: 101325.0
-start_time: null
-definition:
- version: null
- value: null
-title: "XPS Experiment"
-start_time: "2022-04-08T11:47:02.0200Z"
-definition:
- value: "NXmpes"
- version: 1.0
-User:
- name: "Ahmed Mansour"
- email: "amansour@physik.hu-berlin.de"
-Data:
- BE:
- unit: null
-
--
GitLab
From 0cdf8d5d8a8a2704b0d460891ea36f85d6116214 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 17:54:01 +0100
Subject: [PATCH 10/11] Update eln_data and config.
---
docker/xps/example/config_file.json | 55 +++++++++++++++++++++--------
docker/xps/example/eln_data.yaml | 6 +++-
2 files changed, 45 insertions(+), 16 deletions(-)
diff --git a/docker/xps/example/config_file.json b/docker/xps/example/config_file.json
index 2756b2b..155cfda 100644
--- a/docker/xps/example/config_file.json
+++ b/docker/xps/example/config_file.json
@@ -1,17 +1,42 @@
+
{
- "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/description": "hemispherical",
- "/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]/scheme": "Angular dispersive",
- "/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance": "0.0",
- "/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance/@units": "mm",
- "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/type": "Synchrotron X-ray Source",
- "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/probe": "x-ray",
- "/ENTRY[entry]/SAMPLE[sample]/preparation_description": "Sample comes from third party",
- "/ENTRY[entry]/SAMPLE[sample]/temperature": "298",
- "/ENTRY[entry]/SAMPLE[sample]/temperature/@units": "K",
- "/ENTRY[entry]/SAMPLE[sample]/situation": "vacuum",
- "/ENTRY[entry]/SAMPLE[sample]/gas_pressure": "101325",
- "/ENTRY[entry]/SAMPLE[sample]/gas_pressure/@units": "Pa",
- "/ENTRY[entry]/start_time": "2022-04-08T11:47:02.0200Z",
- "/ENTRY[entry]/USER[user]/name": "Ahmed Mansour",
- "/ENTRY[entry]/USER[user]/email": "amansour@physik.hu-berlin.de"
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/description": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/name": "@xps_tocken:analyzer_info/name",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/entrance_slit": "@xps_tocken:region/analyzer_slit",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/scheme": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/pass_energy": "@xps_tocken:region/pass_energy",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/pass_energy/@units": "eV",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/ENERGYDISPERSION[energydispersion]/energy_scan_mode": "@xps_tocken:region/scan_mode/name",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/DATA[data]/raw": "@detector_data:cycles/Cycle_",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/DATA[data]/raw/@units": "counts",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/amplifier_type": "channeltron",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/DETECTOR[detector]/detector_type": "multi-anode",
+"/ENTRY[entry]/INSTRUMENT[instrument]/ELECTRONANALYSER[electronanalyser]/COLLECTIONCOLUMN[collectioncolumn]/scheme": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/distance/@units": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/incident_energy": "@xps_tocken:region/excitation_energy",
+"/ENTRY[entry]/INSTRUMENT[instrument]/BEAM[beam]/incident_energy/@units": "eV",
+"/ENTRY[entry]/INSTRUMENT[instrument]/energy_resolution": "@xps_tocken:region/scan_delta",
+"/ENTRY[entry]/INSTRUMENT[instrument]/energy_resolution/@units": "eV",
+"/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/type": "@eln",
+"/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/name": "@xps_tocken:source_info/name",
+"/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/probe": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/name": "@xps_tocken:parameters/Group",
+"/ENTRY[entry]/SAMPLE[sample]/preparation_description": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/temperature": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/temperature/@units": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/situation": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/gas_pressure": "@eln",
+"/ENTRY[entry]/SAMPLE[sample]/gas_pressure/@units": "@eln",
+"/ENTRY[entry]/DATA[data]/@signal": "",
+"/ENTRY[entry]/DATA[data]/data": "@data:cycles/Cycle_",
+"/ENTRY[entry]/DATA[data]/data/@units": "counts",
+"/ENTRY[entry]/DATA[data]/EB": "counts",
+"/ENTRY[entry]/DATA[data]/EB/@units": "eV",
+"/ENTRY[entry]/title": "@eln",
+"/ENTRY[entry]/start_time": "@eln",
+"/ENTRY[entry]/definition": "@eln",
+"/ENTRY[entry]/definition/@version": "@eln",
+"/ENTRY[entry]/USER[user]/name": "@eln",
+"/ENTRY[entry]/USER[user]/email": "@eln"
}
\ No newline at end of file
diff --git a/docker/xps/example/eln_data.yaml b/docker/xps/example/eln_data.yaml
index bc0ca0e..923bf97 100644
--- a/docker/xps/example/eln_data.yaml
+++ b/docker/xps/example/eln_data.yaml
@@ -2,13 +2,17 @@ Instrument:
Analyser:
Collectioncolumn:
scheme: "Angular dispersive"
+ mode: "Unknown"
description: "hemispherical"
name: null
Energydispersion:
- entrance_slit:
+ entrance_slit: "Unknown"
scheme: "hemispherical"
pass_energy:
unit: null
+ Detector:
+ amplifier_type: "channeltron"
+ detector_type: "Multi-anode"
Beam:
distance:
unit: "mm"
--
GitLab
From 6c3f6d67f6796ea2b9d88ad7542b0ad6f19b1e34 Mon Sep 17 00:00:00 2001
From: RubelMozumder <rubelmozumder@outlook.com>
Date: Wed, 4 Jan 2023 22:08:43 +0100
Subject: [PATCH 11/11] Removing path prefix
---
tools.json | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/tools.json b/tools.json
index 98d2a16..2266ada 100644
--- a/tools.json
+++ b/tools.json
@@ -95,11 +95,11 @@
},
"xps": {
"short_description": "An example for analyzing XPS data.",
- "description": "Includes tools for analyzing XPS spectra and converting SPECS xml files into NeXus.",
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter",
+ "description": "Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS xml files into NeXus.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/xps-jupyter:0.1",
"path_prefix": "lab/tree",
- "mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "icon": "jupyter_logo.svg",
+ "mount_path": "/home/jovyan",
"file_extensions": [
"ipynb",
"nxs",
--
GitLab