diff --git a/docker/ellips/example/ellips.archive.json b/docker/ellips/example/ellips.archive.json
new file mode 100644
index 0000000000000000000000000000000000000000..2038a528e51c59c6430d116da4fcbff34e632191
--- /dev/null
+++ b/docker/ellips/example/ellips.archive.json
@@ -0,0 +1,92 @@
+{
+ "data": {
+ "m_def": "../upload/raw/ellips.scheme.archive.yml#/definitions/section_definitions/0",
+ "reader": "ellips",
+ "nxdl": "NXellipsometry.nxdl",
+ "input_files": [
+ "test-data.data",
+ "eln_data.yaml"
+ ],
+ "output": "SiO2onSi.ellips.nxs",
+ "filename": "test-data.dat",
+ "skip": 3,
+ "sep": "\\t",
+ "colnames": [
+ "type",
+ "wavelength",
+ "angle_of_incidence",
+ "Psi",
+ "Delta",
+ "err.Psi",
+ "err.Delta"
+ ],
+ "derived_parameter_type": "depolarization",
+ "definition": "NXellipsometry",
+ "definition/@version": "0.0.2",
+ "definition/@url": "https://github.com/FAIRmat-NFDI/nexus_definitions/blob/fairmat/contributed_definitions/NXellipsometry.nxdl.xml",
+ "experiment_identifier": "exp-ID",
+ "experiment_description": "RC2 scan on 2nm SiO2 on Si in air",
+ "experiment_type": "NIR-Vis-UV spectroscopic ellipsometry",
+ "plot_name": "Psi and Delta",
+ "start_time": "2022-01-27T03:35:00+00:00",
+ "User": {
+ "name": "Name Surname",
+ "affiliation": "Humboldt-Universität zu Berlin",
+ "address": "Zum Großen Windkanal 2, 12489 Berlin, Germany",
+ "email": "surname.name@physik.hu-berlin.de"
+ },
+ "Instrument": {
+ "model": "RC2",
+ "model/@version": "0.0.1",
+ "company": "J. A. Woollam Co.",
+ "software": "CompleteEASE",
+ "software/version": "6.37",
+ "software/@url": "https://www.jawoollam.com/ellipsometry-software/completeease",
+ "ellipsometer_type": "dual compensator",
+ "rotating_element_type": "compensator (source side)",
+ "calibration_status": "no calibration",
+ "angle_of_incidence/@unit": "degrees",
+ "Beam_path": {
+ "light_source": {
+ "source_type": "arc lamp"
+ },
+ "Detector": {
+ "detector_type": "CCD spectrometer",
+ "count_time": 1
+ },
+ "focussing_probes": {
+ "data_correction": false,
+ "angular_spread": 0.2
+ },
+ "rotating_element": {
+ "revolutions": 50
+ }
+ },
+ "Sample_stage": {
+ "stage_type": "manual stage",
+ "environment_conditions": {
+ "medium": "air"
+ }
+ }
+ },
+ "Sample": {
+ "atom_types": "Si, O",
+ "chemical_formula": "SiO2",
+ "layer_structure": "2nm SiO2 on Si",
+ "sample_name": "2nm SiO2 on Si",
+ "sample_history": "Commercially purchased sample",
+ "sample_type": "multi layer",
+ "substrate": "Si",
+ "backside_roughness": false
+ },
+ "Data": {
+ "data_software": "WVASE",
+ "data_software/version": "3.882",
+ "data_software/@url": "https://www.jawoollam.com/ellipsometry-software/wvase",
+ "data_identifier": 1,
+ "data_type": "Psi/Delta",
+ "spectrum_type": "wavelength",
+ "spectrum_unit": "Angstroms"
+ }
+ }
+}
\ No newline at end of file
diff --git a/docker/ellips/example/ellips.data.archive.json b/docker/ellips/example/ellips.data.archive.json
deleted file mode 100644
index d1420065dbe7f5a945253cd74576948a0538e29a..0000000000000000000000000000000000000000
--- a/docker/ellips/example/ellips.data.archive.json
+++ /dev/null
@@ -1,84 +0,0 @@
-{
- "data": {
- "m_def": "../upload/raw/ellips.scheme.archive.yml#/definitions/section_definitions/0",
- "reader": "ellips",
- "nxdl": "NXellipsometry.nxdl",
- "input_files": [
- "test-data.dat",
- "eln_data.yaml"
- ],
- "output": "SiO2onSi.ellips.nxs",
- "filename": "test-data.dat",
- "skip": 3,
- "sep": "\\t",
- "blocks": [
- "type",
- "angle_of_incidence"
- ],
- "colnames": [
- "type",
- "wavelength",
- "angle_of_incidence",
- "psi",
- "delta",
- "err.psi",
- "err.delta"
- ],
- "x-var": "wavelength",
- "y-var": [
- "psi",
- "delta"
- ],
- "err-var": [
- "err.psi",
- "err.delta"
- ],
- "parameters": [
- "type",
- "angle"
- ],
- "definition": "NXellipsometry",
- "definition/\\@version": "0.0.2",
- "definition/\\@url": "https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat-ellips/contributed_definitions/NXellipsometry.nxdl.xml",
- "experiment_identifier": "exp-ID",
- "experiment_description": "RC2 scan on 2nm SiO2 on Si in air",
- "start_time": "2022-01-27T04:35:00+00:00",
- "acquisition_program/program": "CompleteEASE",
- "acquisition_program/version": "6.37",
- "acquisition_program/\\@url": "https://www.jawoollam.com/ellipsometry-software/completeease",
- "name": "Name Surname",
- "affiliation": "Humboldt-Universität zu Berlin",
- "address": "Zum Großen Windkanal 2, 12489 Berlin, Germany",
- "email": "surname.name@physik.hu-berlin.de",
- "model": "RC2",
- "model/\\@version": "0.0.1",
- "company": "J. A. Woollam Co.",
- "firmware": "WVASE",
- "firmware/\\@version": "3.882",
- "firmware/\\@url": "https://www.jawoollam.com/ellipsometry-software/wvase",
- "light_source": "arc lamp",
- "focussing_probes": false,
- "angular_spread": 0.2,
- "ellipsometry_type": "dual compensator",
- "calibration_status": "no calibration",
- "stage_type": "manual stage",
- "detector_type": "CCD spectrometer",
- "count_time": 1,
- "integration_time": 0,
- "rotating_element": "compensator (source side)",
- "atom_types": "Si, O",
- "sample_name": "2nm SiO2 on Si",
- "sample_history": "Commercially purchased sample",
- "layer_structure": "2nm SiO2 on Si",
- "data_identifier": 1,
- "data_type": "psi/delta",
- "medium": "air",
- "column_names": [
- "psi",
- "delta"
- ],
- "angle_of_incidence_unit": "degrees",
- "wavelength_unit": "angstrom"
- },
- "m_ref_archives": {}
-}
\ No newline at end of file
diff --git a/docker/ellips/example/ellips.scheme.archive.yml b/docker/ellips/example/ellips.scheme.archive.yml
index bf4896885ee9005ffb2a98a5b5142322dd5c9ef1..28bd299980a3b879868a11237c5f9092974a7072 100644
--- a/docker/ellips/example/ellips.scheme.archive.yml
+++ b/docker/ellips/example/ellips.scheme.archive.yml
@@ -20,8 +20,9 @@ definitions:
component: StringEditQuantity
skip:
type: int
- description: "Enter how many rows should be skipped, i.e. the number
- of lines in the header of the data file."
+ description: |
+ Enter how many rows should be skipped, i.e. the number
+ of lines in the header of the data file.
m_annotations:
eln:
minValue: 0
@@ -32,71 +33,37 @@ definitions:
m_annotations:
eln:
component: StringEditQuantity
- blocks:
- type: str
- description: "Names of the blocks in the data file.
- If the data file is separated into blocks, e.g. if
- the first n rows after the header contain data obtained
- at a certain angle of incidence, the rows from n+1 to 2n
- containt data obtained at another angle of incidence
- etc. one block name could be 'angle_of_incidence'. If
- the data file contains more than one type of data, e.g.
- ellipsometric angles and depolarization, a block name
- could be 'type'."
- shape: ["*"]
- m_annotations:
- eln:
- component: StringEditQuantity
colnames:
type: str
- description: Names of the columns in the data file.
+ description: "Names of the columns in the data file."
shape: ["*"]
m_annotations:
eln:
component: StringEditQuantity
- x-var:
+ derived_parameter_type:
type: str
- description: Name of the x-variable, e.g. wavelength or energy.
- m_annotations:
- eln:
- component: StringEditQuantity
- y-var:
- type: str
- description: Name(s) of the measured quantity, e.g. psi and Delta.
- shape: ["*"]
- m_annotations:
- eln:
- component: StringEditQuantity
- err-var:
- type: str
- description: Names of the errors corresponding to y-var.
- shape: ["*"]
- m_annotations:
- eln:
- component: StringEditQuantity
- parameters:
- type: str
- description: Parameter names; similar or the same as the blocks.
- shape: ["*"]
+ description: |
+ Type of parameters that were derived from the
+ measured data, e.g. depolarization.
m_annotations:
eln:
component: StringEditQuantity
definition:
type: str
- description: "Name of the application definition (NXellipsometry).
- All other meta data below are described in the
- [NXellipsometry application definition]
- (https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html)."
+ description: |
+ Name of the application definition (NXellipsometry).
+ All other meta data below are described in the
+ [NXellipsometry application definition]
+ (https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html).
m_annotations:
eln:
component: StringEditQuantity
- # ToDo: Remove @notation which does not work
- definition/\@version:
+ definition/@version:
type: str
m_annotations:
eln:
component: StringEditQuantity
- definition/\@url:
+ definition/@url:
type: str
m_annotations:
eln:
@@ -111,181 +78,263 @@ definitions:
m_annotations:
eln:
component: StringEditQuantity
- start_time:
- type: Datetime
- m_annotations:
- eln:
- component: DateTimeEditQuantity
- acquisition_program/program:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- acquisition_program/version:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- acquisition_program/\@url:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- name:
+ experiment_type:
type: str
m_annotations:
eln:
component: StringEditQuantity
- affiliation:
+ plot_name:
type: str
+ description: "Name of the default plot"
m_annotations:
eln:
- component: StringEditQuantity
- address:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- email:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- model:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- model/\@version:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- company:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- firmware:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- firmware/\@version:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- firmware/\@url:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- light_source:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- focussing_probes:
- type: bool
- m_annotations:
- eln:
- component: BoolEditQuantity
- angular_spread:
- type: np.float64
- unit: radian
- m_annotations:
- eln:
- component: NumberEditQuantity
- ellipsometry_type:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- calibration_status:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- stage_type:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- detector_type:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- count_time:
- type: np.float64
- unit: second
- m_annotations:
- eln:
- component: NumberEditQuantity
- minValue: 0
- defaultDisplayUnit: "s"
- integration_time:
- type: np.float64
- unit: second
- m_annotations:
- eln:
- component: NumberEditQuantity
minValue: 0
- defaultDisplayUnit: "s"
- rotating_element:
- type: str
- m_annotations:
- eln:
component: StringEditQuantity
- atom_types:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- sample_name:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- sample_history:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- layer_structure:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- data_identifier:
- type: int
- m_annotations:
- eln:
- component: NumberEditQuantity
- data_type:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- medium:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- column_names:
- type: str
- shape: ["*"]
- m_annotations:
- eln:
- component: StringEditQuantity
- angle_of_incidence_unit:
- type: str
- m_annotations:
- eln:
- component: StringEditQuantity
- wavelength_unit:
- type: str
+ start_time:
+ type: Datetime
m_annotations:
eln:
- component: StringEditQuantity
+ component: DateTimeEditQuantity
+ sub_sections:
+ User:
+ section:
+ m_annotations:
+ eln:
+ overview: true
+ quantities:
+ name:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ affiliation:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ address:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ email:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ Instrument:
+ section:
+ m_annotations:
+ eln:
+ overview: true
+ quantities:
+ model:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ model/@version:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ company:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ software:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ software/version:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ software/@url:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ ellipsometer_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ rotating_element_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ calibration_status:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ angle_of_incidence/@unit:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ sub_sections:
+ Beam_path:
+ section:
+ sub_sections:
+ light_source:
+ section:
+ quantities:
+ source_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ Detector:
+ section:
+ quantities:
+ detector_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ count_time:
+ type: np.float64
+ unit: second
+ m_annotations:
+ eln:
+ component: NumberEditQuantity
+ minValue: 0
+ defaultDisplayUnit: "s"
+ focussing_probes:
+ section:
+ quantities:
+ data_correction:
+ type: bool
+ m_annotations:
+ eln:
+ component: BoolEditQuantity
+ angular_spread:
+ type: np.float64
+ unit: radian
+ m_annotations:
+ eln:
+ component: NumberEditQuantity
+ defaultDisplayUnit: "rad"
+ rotating_element:
+ section:
+ quantities:
+ revolutions:
+ type: np.float64
+ m_annotations:
+ eln:
+ component: NumberEditQuantity
+ Sample_stage:
+ section:
+ quantities:
+ stage_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ sub_sections:
+ environment_conditions:
+ section:
+ quantities:
+ medium:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ Sample:
+ section:
+ m_annotations:
+ eln:
+ overview: true
+ quantities:
+ atom_types:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ backside_roughness:
+ type: bool
+ m_annotations:
+ eln:
+ component: BoolEditQuantity
+ chemical_formula:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+
+ layer_structure:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ sample_name:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ sample_history:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ sample_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ substrate:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ Data:
+ section:
+ m_annotations:
+ eln:
+ overview: true
+ quantities:
+ data_software:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ data_software/version:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ data_software/@url:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ data_identifier:
+ type: int
+ m_annotations:
+ eln:
+ component: NumberEditQuantity
+ data_type:
+ type: str
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ spectrum_type:
+ type: str
+ description: |
+ Type of the spectral values (x-axis of the data),
+ e.g. wavelength, energy etc.
+ m_annotations:
+ eln:
+ component: StringEditQuantity
+ spectrum_unit:
+ type: str
+ description: "Unit of the spectral values (x-axis of the data)"
+ m_annotations:
+ eln:
+ component: StringEditQuantity
diff --git a/docker/ellips/example/eln_data.yaml b/docker/ellips/example/eln_data.yaml
index d253621580e5f32efe4a5f904e10b7954590141b..70b708ef36af68e1508c09510f8836b4a4e8edf6 100644
--- a/docker/ellips/example/eln_data.yaml
+++ b/docker/ellips/example/eln_data.yaml
@@ -1,71 +1,72 @@
-acquisition_program/\@url: https://www.jawoollam.com/ellipsometry-software/completeease
-acquisition_program/program: CompleteEASE
-acquisition_program/version: '6.37'
-address: Zum Großen Windkanal 2, 12489 Berlin, Germany
-affiliation: Humboldt-Universität zu Berlin
-angle_of_incidence_unit: degrees
-angular_spread:
- unit: rad
- value: 0.2
-atom_types: Si, O
-blocks:
-- type
-- angle_of_incidence
-calibration_status: no calibration
+Data:
+ data_identifier: 1
+ data_software: WVASE
+ data_software/@url: https://www.jawoollam.com/ellipsometry-software/wvase
+ data_software/version: '3.882'
+ data_type: Psi/Delta
+ spectrum_type: wavelength
+ spectrum_unit: Angstroms
+Instrument:
+ Beam_path:
+ Detector:
+ count_time:
+ unit: s
+ value: 1.0
+ detector_type: CCD spectrometer
+ focussing_probes:
+ angular_spread:
+ unit: rad
+ value: 0.2
+ data_correction: false
+ light_source:
+ source_type: arc lamp
+ rotating_element:
+ revolutions: 50.0
+ Sample_stage:
+ environment_conditions:
+ medium: air
+ stage_type: manual stage
+ angle_of_incidence/@unit: degrees
+ calibration_status: no calibration
+ company: J. A. Woollam Co.
+ ellipsometer_type: dual compensator
+ model: RC2
+ model/@version: 0.0.1
+ rotating_element_type: compensator (source side)
+ software: CompleteEASE
+ software/@url: https://www.jawoollam.com/ellipsometry-software/completeease
+ software/version: '6.37'
+Sample:
+ atom_types: Si, O
+ backside_roughness: false
+ chemical_formula: SiO2
+ layer_structure: 2nm SiO2 on Si
+ sample_history: Commercially purchased sample
+ sample_name: 2nm SiO2 on Si
+ sample_type: multi layer
+ substrate: Si
+User:
+ address: Zum Großen Windkanal 2, 12489 Berlin, Germany
+ affiliation: Humboldt-Universität zu Berlin
+ email: surname.name@physik.hu-berlin.de
+ name: Name Surname
colnames:
- type
- wavelength
- angle_of_incidence
-- psi
-- delta
-- err.psi
-- err.delta
-column_names:
-- psi
-- delta
-company: J. A. Woollam Co.
-count_time:
- unit: s
- value: 1
-data_identifier: 1
-data_type: psi/delta
+- Psi
+- Delta
+- err.Psi
+- err.Delta
definition: NXellipsometry
-definition/\@url: https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat-ellips/contributed_definitions/NXellipsometry.nxdl.xml
-definition/\@version: 0.0.2
-detector_type: CCD spectrometer
-ellipsometry_type: dual compensator
-email: surname.name@physik.hu-berlin.de
-err-var:
-- err.psi
-- err.delta
+definition/@url: https://github.com/FAIRmat-NFDI/nexus_definitions/blob/fairmat/contributed_definitions/NXellipsometry.nxdl.xml
+definition/@version: 0.0.2
+derived_parameter_type: depolarization
experiment_description: RC2 scan on 2nm SiO2 on Si in air
experiment_identifier: exp-ID
+experiment_type: NIR-Vis-UV spectroscopic ellipsometry
filename: test-data.dat
-firmware: WVASE
-firmware/\@url: https://www.jawoollam.com/ellipsometry-software/wvase
-firmware/\@version: '3.882'
-focussing_probes: false
-integration_time:
- unit: s
- value: 0
-layer_structure: 2nm SiO2 on Si
-light_source: arc lamp
-medium: air
-model: RC2
-model/\@version: 0.0.1
-name: Name Surname
-parameters:
-- type
-- angle
-rotating_element: compensator (source side)
-sample_history: Commercially purchased sample
-sample_name: 2nm SiO2 on Si
+plot_name: Psi and Delta
sep: \t
skip: 3
-stage_type: manual stage
-start_time: '2022-01-27T04:35:00+00:00'
-wavelength_unit: angstrom
-x-var: wavelength
-y-var:
-- psi
-- delta
+start_time: '2022-01-27T03:35:00+00:00'
\ No newline at end of file
diff --git a/docker/ellips/requirements.in b/docker/ellips/requirements.in
index be96c194cb80db897a3499bc6c908f7fff3bb05b..8aa11bc6e667ec54bbdf3d218b7acae56155db85 100644
--- a/docker/ellips/requirements.in
+++ b/docker/ellips/requirements.in
@@ -1,4 +1,4 @@
-pynxtools>=0.0.2
+pynxtools>=0.0.3
ipywidgets<8.0.0,>=7.0.1
nodejs
h5glance>=0.8
@@ -8,4 +8,4 @@ jupyterlab_h5web[full]>=6.0.0
punx>=0.2.5
plotly
ipython
-pyElli[fitting]
+pyElli[fitting]>=0.17.0
diff --git a/docker/ellips/requirements.txt b/docker/ellips/requirements.txt
index b4358e2538a26e9131a727d7dde1d22598c09aa3..335dab81e3a671db2876590f282d63aca6eb2bb4 100644
--- a/docker/ellips/requirements.txt
+++ b/docker/ellips/requirements.txt
@@ -4,7 +4,7 @@
#
# pip-compile --output-file=requirements.txt --resolver=backtracking
#
-anyio==3.6.2
+anyio==3.7.0
# via jupyter-server
argon2-cffi==21.3.0
# via
@@ -34,7 +34,7 @@ beautifulsoup4==4.12.2
# via nbconvert
bleach==6.0.0
# via nbconvert
-cattrs==22.2.0
+cattrs==23.1.2
# via requests-cache
certifi==2023.5.7
# via requests
@@ -50,11 +50,11 @@ cloudpickle==2.2.1
# via dask
comm==0.1.3
# via ipykernel
-contourpy==1.0.7
+contourpy==1.1.0
# via matplotlib
cycler==0.11.0
# via matplotlib
-dask[array]==2023.4.1
+dask[array]==2023.6.0
# via
# hyperspy
# kikuchipy
@@ -73,7 +73,7 @@ diffpy-structure==3.1.0
# diffsims
# kikuchipy
# orix
-diffsims==0.5.1
+diffsims==0.5.2
# via
# kikuchipy
# pyxem
@@ -82,20 +82,22 @@ dill==0.3.6
entrypoints==0.4
# via ipyparallel
exceptiongroup==1.1.1
- # via cattrs
+ # via
+ # anyio
+ # cattrs
executing==1.2.0
# via stack-data
fabio==2023.4.1
# via
# pyfai
# silx
-fastjsonschema==2.16.3
+fastjsonschema==2.17.1
# via nbformat
flatdict==4.0.1
# via pynxtools
-fonttools==4.39.3
+fonttools==4.40.0
# via matplotlib
-fsspec==2023.5.0
+fsspec==2023.6.0
# via
# dask
# hyperspy
@@ -120,13 +122,14 @@ h5py==3.8.0
# ifes-apt-tc-data-modeling
# jupyterlab-h5web
# kikuchipy
+ # nionswift
# orix
# punx
# pyelli
# pyfai
# pynxtools
# silx
-hdf5plugin==4.1.1
+hdf5plugin==4.1.2
# via jupyterlab-h5web
htmlgen==2.0.0
# via h5glance
@@ -145,6 +148,9 @@ imageio==2.27.0
# via
# hyperspy
# kikuchipy
+ # nionswift
+ # nionswift-io
+ # nionui
# scikit-image
importlib-metadata==6.6.0
# via
@@ -152,7 +158,7 @@ importlib-metadata==6.6.0
# hyperspy
importlib-resources==5.12.0
# via pyelli
-ipykernel==6.23.0
+ipykernel==6.23.2
# via
# ipyparallel
# ipywidgets
@@ -160,7 +166,7 @@ ipykernel==6.23.0
# notebook
ipyparallel==8.6.1
# via hyperspy
-ipython==8.13.2
+ipython==8.14.0
# via
# -r requirements.in
# hyperspy
@@ -192,7 +198,7 @@ jinja2==3.1.2
# notebook
joblib==1.2.0
# via scikit-learn
-json5==0.9.11
+json5==0.9.14
# via jupyterlab-server
jsonschema==4.17.3
# via
@@ -206,7 +212,7 @@ jupyter-client==8.2.0
# nbclassic
# nbclient
# notebook
-jupyter-core==5.3.0
+jupyter-core==5.3.1
# via
# ipykernel
# jupyter-client
@@ -229,18 +235,18 @@ jupyterlab==3.5.3
# -r requirements.in
# ifes-apt-tc-data-modeling
# pynxtools
-jupyterlab-h5web[full]==7.1.1
+jupyterlab-h5web[full]==8.0.0
# via
# -r requirements.in
# ifes-apt-tc-data-modeling
# pynxtools
jupyterlab-pygments==0.2.2
# via nbconvert
-jupyterlab-server==2.22.1
+jupyterlab-server==2.23.0
# via jupyterlab
jupyterlab-widgets==1.1.4
# via ipywidgets
-kikuchipy==0.8.4
+kikuchipy==0.8.6
# via pynxtools
kiwisolver==1.4.4
# via matplotlib
@@ -250,7 +256,7 @@ lark==1.1.5
# pynxtools
lazy-loader==0.2
# via scikit-image
-llvmlite==0.40.0
+llvmlite==0.40.1rc1
# via numba
lmfit==1.2.1
# via
@@ -262,7 +268,7 @@ lxml==4.9.2
# via
# punx
# pyresttable
-markupsafe==2.1.2
+markupsafe==2.1.3
# via
# jinja2
# nbconvert
@@ -294,14 +300,14 @@ nbclassic==1.0.0
# via
# jupyterlab
# notebook
-nbclient==0.7.4
+nbclient==0.8.0
# via nbconvert
-nbconvert==7.4.0
+nbconvert==7.5.0
# via
# jupyter-server
# nbclassic
# notebook
-nbformat==5.8.0
+nbformat==5.9.0
# via
# jupyter-server
# nbclassic
@@ -317,6 +323,22 @@ networkx==3.1
# via
# radioactivedecay
# scikit-image
+niondata==0.15.3
+ # via
+ # nionswift
+ # nionswift-io
+nionswift==0.16.8
+ # via pynxtools
+nionswift-io==0.15.1
+ # via nionswift
+nionui==0.6.10
+ # via nionswift
+nionutils==0.4.6
+ # via
+ # niondata
+ # nionswift
+ # nionswift-io
+ # nionui
nodejs==0.1.1
# via -r requirements.in
notebook==6.5.4
@@ -352,6 +374,10 @@ numpy==1.24.3
# kikuchipy
# lmfit
# matplotlib
+ # niondata
+ # nionswift
+ # nionswift-io
+ # nionui
# numba
# numexpr
# numpy-quaternion
@@ -381,7 +407,7 @@ orix==0.11.1
# diffsims
# kikuchipy
# pyxem
-orjson==3.8.12
+orjson==3.9.1
# via h5grove
packaging==23.1
# via
@@ -397,7 +423,7 @@ packaging==23.1
# pooch
# scikit-image
# xarray
-pandas==2.0.1
+pandas==2.0.2
# via
# ifes-apt-tc-data-modeling
# pyelli
@@ -417,17 +443,18 @@ pillow==9.5.0
# via
# imageio
# matplotlib
+ # nionswift
# scikit-image
-pint==0.21
+pint==0.22
# via
# hyperspy
# pyelli
-platformdirs==3.5.0
+platformdirs==3.5.3
# via
# jupyter-core
# pooch
# requests-cache
-plotly==5.14.1
+plotly==5.15.0
# via
# -r requirements.in
# pyelli
@@ -435,9 +462,9 @@ pooch==1.7.0
# via
# kikuchipy
# orix
-prettytable==3.7.0
+prettytable==3.8.0
# via hyperspy
-prometheus-client==0.16.0
+prometheus-client==0.17.0
# via
# jupyter-server
# nbclassic
@@ -462,15 +489,15 @@ pycifrw==4.4.5
# via diffpy-structure
pycparser==2.21
# via cffi
-pyelli[fitting]==0.16.0
+pyelli[fitting]==0.17.0
# via -r requirements.in
-pyfai==2023.3.0
+pyfai==2023.5.0
# via pyxem
pygments==2.15.1
# via
# ipython
# nbconvert
-pynxtools==0.0.2
+pynxtools==0.0.3
# via -r requirements.in
pyparsing==3.0.9
# via matplotlib
@@ -487,11 +514,14 @@ python-dateutil==2.8.2
# pandas
pytz==2023.3
# via
+ # nionswift
# pandas
# pynxtools
+pytz-deprecation-shim==0.1.0.post0
+ # via tzlocal
pywavelets==1.4.1
# via scikit-image
-pyxem==0.15.0
+pyxem==0.15.1
# via pynxtools
pyyaml==6.0
# via
@@ -500,7 +530,7 @@ pyyaml==6.0
# kikuchipy
# pyelli
# pynxtools
-pyzmq==25.0.2
+pyzmq==25.1.0
# via
# ipykernel
# ipyparallel
@@ -510,9 +540,9 @@ pyzmq==25.0.2
# notebook
radioactivedecay==0.4.17
# via ifes-apt-tc-data-modeling
-rapidfuzz==3.0.0
+rapidfuzz==3.1.1
# via pyelli
-requests==2.30.0
+requests==2.31.0
# via
# hyperspy
# jupyterlab-server
@@ -522,7 +552,7 @@ requests==2.30.0
# requests-cache
requests-cache==1.0.1
# via pynxtools
-scikit-image==0.20.0
+scikit-image==0.21.0
# via
# hyperspy
# kikuchipy
@@ -538,6 +568,8 @@ scipy==1.10.1
# hyperspy
# kikuchipy
# lmfit
+ # niondata
+ # nionswift
# orix
# pyelli
# pyfai
@@ -571,7 +603,7 @@ sparse==0.14.0
# via hyperspy
stack-data==0.6.2
# via ipython
-sympy==1.11.1
+sympy==1.12
# via
# hyperspy
# radioactivedecay
@@ -598,7 +630,7 @@ toolz==0.12.0
# dask
# hyperspy
# partd
-tornado==6.3.1
+tornado==6.3.2
# via
# ipykernel
# ipyparallel
@@ -637,13 +669,23 @@ transforms3d==0.4.1
# via
# diffsims
# pyxem
+typing-extensions==4.6.3
+ # via
+ # cattrs
+ # pint
tzdata==2023.3
- # via pandas
+ # via
+ # pandas
+ # pytz-deprecation-shim
+tzlocal==4.3
+ # via
+ # nionswift
+ # pynxtools
uncertainties==3.1.7
# via lmfit
url-normalize==1.4.3
# via requests-cache
-urllib3==2.0.2
+urllib3==2.0.3
# via
# requests
# requests-cache
@@ -655,11 +697,11 @@ webencodings==0.5.1
# via
# bleach
# tinycss2
-websocket-client==1.5.1
+websocket-client==1.5.3
# via jupyter-server
widgetsnbextension==3.6.4
# via ipywidgets
-xarray==2023.4.2
+xarray==2023.5.0
# via pynxtools
zipfile37==0.1.3
# via pynxtools