Extensions for EM and APM for use cases from FAU Erlangen-Nuremberg CENEM and APM run-through NFDI-MatWerk (#421)

* Exemplar alternative strategy to keep track of projects

* ran a make style, must have been a while ago since this was done the last time

* Add minimal example electron tomography

* spellchecking

* NXcollection to store flat collection of metadata that people have several times requested but for which we currently have no mapping to NeXus or we do not know exactly whats behind these parameters

* align styling and formatting with apm_prepare_nomad_v142 branch

* Apm prepare nomad v142 (#424)

* Adding concepts for sampled monitoring instances as stored in rhit and hits

* add precommit config and removed unnecessary categories in custom-dictionary

* intend NXdata monitoring instances under measurement, install pre-commit

---------

Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>

* align linting, styling, and formatting with niac PR1626

* automation script to populate the dictionary in case of precommit failing on new words

* Shortening and tightening cover page updating also

* Shortening and tightening completed, added also definition of versions

* corrections on fairmat cover

* edit in reviewer comments

* bump isort in precommit

---------

Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>

Author: mkuehbach

.cspell/custom-dictionary.txt

@@ -0,0 +1,27 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 26.3.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.3.0
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/pycqa/isort
+    rev: 8.0.1
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/streetsidesoftware/cspell-cli
+    rev: v9.7.0
+    hooks:
+      - id: cspell  # spellchecking
+        pass_filenames: false
+        args:
+          - --config
+          - cspell.json
+          - applications/**/*
+          - base_classes/**/*
+          - contributed_definitions/**/*

.pre-commit-config.yaml

@@ -48,13 +48,13 @@ install ::
 	$(PYTHON) -m pip install -r requirements.txt
 
 style ::
-	$(PYTHON) -m black --check dev_tools
-	$(PYTHON) -m flake8 dev_tools
-	$(PYTHON) -m isort --check dev_tools
+	$(PYTHON) -m black --check .
+	$(PYTHON) -m flake8 .
+	$(PYTHON) -m isort --check .
 
 autoformat ::
-	$(PYTHON) -m black dev_tools
-	$(PYTHON) -m isort dev_tools
+	$(PYTHON) -m black .
+	$(PYTHON) -m isort .
 
 test ::
 	$(PYTHON) -m pytest dev_tools

Makefile

@@ -251,6 +251,9 @@
             <field name="checksum" type="NX_CHAR" recommended="true"/>
             <field name="algorithm" type="NX_CHAR" recommended="true"/>
         </group>
+        <group name="project" type="NXproject" optional="true">
+            <field name="name" type="NX_CHAR"/>
+        </group>
         <group name="userID" type="NXuser" minOccurs="0" maxOccurs="unbounded" nameType="partial">
             <doc>
                 Information about persons who performed or were involved in the microscope
@@ -1587,6 +1590,12 @@ basically optional use of NXaberration therein at least some value required-->
                     <group name="sensorID" type="NXsensor" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
                     <group name="actuatorID" type="NXactuator" nameType="partial" minOccurs="0" maxOccurs="unbounded"/>
                 </group>
+                <group type="NXcollection" optional="true">
+                    <doc>
+                        Group with content not meant for validation to store e.g.,
+                        metadata that are currently not standardized with NeXus.
+                    </doc>
+                </group>
             </group>
         </group>
         <group name="simulation" type="NXem_simulation" optional="true">
@@ -1872,6 +1881,63 @@ not wish to duplicate all payload data-->
                 </group>
             </group>
             <group name="eels" type="NXem_eels" optional="true"/>
+            <group name="tomo" type="NXprocess" optional="true">
+                <doc>
+                    Electron tomography
+                </doc>
+                <group name="reconstructionID" type="NXprocess" nameType="partial" minOccurs="0" maxOccurs="unbounded">
+                    <doc>
+                        Processing a single tilt series into an electron tomogram
+                    </doc>
+                    <group name="configuration" type="NXparameters" recommended="true">
+                        <doc>
+                            Parameters used for computing the tomogram.
+                        </doc>
+                    </group>
+                    <group name="programID" type="NXprogram" nameType="partial" recommended="true">
+                        <doc>
+                            The program with which the reconstruction was performed.
+                        </doc>
+                        <field name="program" type="NX_CHAR">
+                            <attribute name="version" type="NX_CHAR" recommended="true"/>
+                        </field>
+                    </group>
+                    <group name="tomogram" type="NXdata">
+                        <doc>
+                            The resulting tomogram
+                        </doc>
+                        <attribute name="signal" type="NX_CHAR"/>
+                        <attribute name="axes" type="NX_CHAR"/>
+                        <attribute name="AXISNAME_indices" type="NX_UINT" nameType="partial"/>
+                        <field name="title" type="NX_CHAR" recommended="true"/>
+                        <field name="intensity" type="NX_NUMBER">
+                            <dimensions rank="3">
+                                <dim index="1" value="n_k"/>
+                                <dim index="2" value="n_j"/>
+                                <dim index="3" value="n_i"/>
+                            </dimensions>
+                        </field>
+                        <field name="axis_k" type="NX_FLOAT">
+                            <dimensions rank="1">
+                                <dim index="1" value="n_k"/>
+                            </dimensions>
+                            <attribute name="long_name" type="NX_CHAR"/>
+                        </field>
+                        <field name="axis_j" type="NX_FLOAT">
+                            <dimensions rank="1">
+                                <dim index="1" value="n_j"/>
+                            </dimensions>
+                            <attribute name="long_name" type="NX_CHAR"/>
+                        </field>
+                        <field name="axis_i" type="NX_FLOAT">
+                            <dimensions rank="1">
+                                <dim index="1" value="n_i"/>
+                            </dimensions>
+                            <attribute name="long_name" type="NX_CHAR"/>
+                        </field>
+                    </group>
+                </group>
+            </group>
         </group>
     </group>
     <!--see an example how to map e.g. the following flat schema https://www.zenodo.org/record/6513745 to NXem