Fairmat 2023

.github/workflows/ci.yaml

@@ -72,6 +72,7 @@ jobs:
             texlive-latex-recommended \
             texlive-latex-extra \
             texlive-fonts-recommended
+          tex --version
 
       - name: Generate build files
         env:

contributed_definitions/NXaberration.nxdl.xml

@@ -1,79 +1,55 @@
-<?xml version="1.0" ?>
+<?xml version="1.0" encoding="UTF-8"?>
 <?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
-<definition category="base" extends="NXobject" name="NXaberration" type="group" xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+# 
+# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
+# 
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# For further information, see http://www.nexusformat.org
+-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" extends="NXobject" name="NXaberration" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <doc>
-         Models for aberrations of electro-magnetic lenses in electron microscopy.
-
-         The notation follows `O. Krivanek et al. (1999) &lt;https://doi.org/10.1016/S0304-3991(99)00013-3&gt;`_
-         and `O. Krivanek et al. (2003) &lt;https://doi.org/10.1016/S0304-3991(03)00090-1&gt;`_
-         See also `S. J. Pennycock and P. D. Nellist &lt;https://doi.org/10.1007/978-1-4419-7200-2&gt;`_ (page 44ff, and page 118ff)
-         for further details, additional literature, and the unit of the coefficients.
-         Consult Table 7-2 of Ibid. publication on how to convert between
-         conventions of different groups/vendors.
+         Quantified aberration coefficient in an aberration_model.
     </doc>
-    <field name="c_1_0" type="NX_FLOAT" units="NX_LENGTH">
+    <field name="magnitude" type="NX_FLOAT" units="NX_LENGTH"/>
+    <field name="uncertainty" type="NX_FLOAT" units="NX_LENGTH">
         <doc>
-             Defocus
+             Confidence
         </doc>
     </field>
-    <field name="c_1_2_a" type="NX_FLOAT" units="NX_LENGTH">
+    <field name="uncertainty_model">
         <doc>
-             Two-fold astigmatism
+             How was the uncertainty quantified e.g. via the 95% confidence interval.
         </doc>
     </field>
-    <field name="c_1_2_b" type="NX_FLOAT" units="NX_LENGTH">
+    <field name="delta_time" type="NX_FLOAT" units="NX_TIME">
         <doc>
-             Two-fold astigmatism
+             Time elapsed since the last measurement.
         </doc>
     </field>
-    <field name="c_2_1_a" type="NX_FLOAT" units="NX_LENGTH">
+    <field name="angle" type="NX_FLOAT" units="NX_ANGLE">
         <doc>
-             Second-order axial coma
-        </doc>
-    </field>
-    <field name="c_2_1_b" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Second-order axial coma
-        </doc>
-    </field>
-    <field name="c_2_3_a" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Threefold astigmatism
-        </doc>
-    </field>
-    <field name="c_2_3_b" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Threefold astigmatism
-        </doc>
-    </field>
-    <field name="c_3_0" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Spherical aberration
-        </doc>
-    </field>
-    <field name="c_3_2_a" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Star aberration
-        </doc>
-    </field>
-    <field name="c_3_2_b" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Star aberration
-        </doc>
-    </field>
-    <field name="c_3_4_a" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Fourfold astigmatism
-        </doc>
-    </field>
-    <field name="c_3_4_b" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Fourfold astigmatism
-        </doc>
-    </field>
-    <field name="c_5_0" type="NX_FLOAT" units="NX_LENGTH">
-        <doc>
-             Fifth-order spherical aberration
+             For the CEOS definitions the C aberrations are radial-symmetric and have no
+             angle entry, while the A, B, D, S, or R aberrations are n-fold
+             symmetric and have an angle entry.
+             For the NION definitions the coordinate system differs to the one
+             used in CEOS and instead two aberration coefficients a and b are used.
         </doc>
     </field>
+    <field name="name"/>
+    <field name="alias"/>
 </definition>

contributed_definitions/NXaberration_model.nxdl.xml

@@ -0,0 +1,105 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+# 
+# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
+# 
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# For further information, see http://www.nexusformat.org
+-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" extends="NXobject" name="NXaberration_model" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <doc>
+         Models for aberrations of electro-magnetic lenses in electron microscopy.
+
+         See `S. J. Pennycock and P. D. Nellist &lt;https://doi.org/10.1007/978-1-4419-7200-2&gt;`_ (page 44ff, and page 118ff)
+         for different definitions available and further details. Table 7-2 of Ibid.
+         publication (page 305ff) documents how to convert from the NION to the 
+         CEOS definitions.
+    </doc>
+    <field name="model">
+        <enumeration>
+            <item value="ceos"/>
+            <item value="nion"/>
+        </enumeration>
+    </field>
+    <group type="NXaberration"/>
+    <field name="c_1_0" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Defocus
+        </doc>
+    </field>
+    <field name="c_1_2_a" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Two-fold astigmatism
+        </doc>
+    </field>
+    <field name="c_1_2_b" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Two-fold astigmatism
+        </doc>
+    </field>
+    <field name="c_2_1_a" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Second-order axial coma
+        </doc>
+    </field>
+    <field name="c_2_1_b" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Second-order axial coma
+        </doc>
+    </field>
+    <field name="c_2_3_a" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Threefold astigmatism
+        </doc>
+    </field>
+    <field name="c_2_3_b" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Threefold astigmatism
+        </doc>
+    </field>
+    <field name="c_3_0" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Spherical aberration
+        </doc>
+    </field>
+    <field name="c_3_2_a" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Star aberration
+        </doc>
+    </field>
+    <field name="c_3_2_b" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Star aberration
+        </doc>
+    </field>
+    <field name="c_3_4_a" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Fourfold astigmatism
+        </doc>
+    </field>
+    <field name="c_3_4_b" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Fourfold astigmatism
+        </doc>
+    </field>
+    <field name="c_5_0" type="NX_FLOAT" units="NX_LENGTH">
+        <doc>
+             Fifth-order spherical aberration
+        </doc>
+    </field>
+</definition>

contributed_definitions/NXaberration_model_ceos.nxdl.xml

@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+# 
+# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
+# 
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# For further information, see http://www.nexusformat.org
+-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" extends="NXobject" name="NXaberration_model_ceos" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <doc>
+         CEOS definitions/model for aberrations of electro-magnetic lenses.
+
+         See `S. J. Pennycock and P. D. Nellist &lt;https://doi.org/10.1007/978-1-4419-7200-2&gt;`_ (page 44ff, and page 118ff)
+         for different definitions available and further details. Table 7-2 of Ibid.
+         publication (page 305ff) documents how to convert from the NION to the 
+         CEOS definitions.
+    </doc>
+    <field name="model">
+        <enumeration>
+            <item value="ceos"/>
+        </enumeration>
+    </field>
+    <group name="c_1" type="NXaberration"/>
+    <group name="a_1" type="NXaberration"/>
+    <group name="b_2" type="NXaberration"/>
+    <group name="a_2" type="NXaberration"/>
+    <group name="c_3" type="NXaberration"/>
+    <group name="s_3" type="NXaberration"/>
+    <group name="a_3" type="NXaberration"/>
+    <!--based on feedback from Thilo Remmele the following aberrations could be measured (enhanced mode, tilt angle > 30 mrad) but are not corrected-->
+    <group name="b_4" type="NXaberration"/>
+    <group name="d_4" type="NXaberration"/>
+    <group name="a_4" type="NXaberration"/>
+    <group name="c_5" type="NXaberration"/>
+    <group name="s_5" type="NXaberration"/>
+    <group name="r_5" type="NXaberration"/>
+    <group name="a_6" type="NXaberration"/>
+    <!--further comments from Thilo Remmele (Leibniz-Institut für Kristallzüchtung)
+ThermoFisher uses CEOS correctors but makes customizations to these in their microscopes
+Aberration naming schema: C_order_multiplicity (similar to NXem, but with
+another coordinate system and in addition with a confidence entry.
+Aberrations with multiplicity 0 have no angle entry (C1,C3,C5,.., CEOS notation)
+contrast transferfuntion: ctf = e^(-i*Xi(g)) in Fourier space
+aberration function:
+Xi(g) = 2*pi/lamda{ 1/2 * (lamda*g)^2 (C20 + C22 cos[2(phi-phi_22)]
+                   +1/3 * (lamda*g)^3 (C31 cos[(phi-phi_31) + C33 cos[3(phi-phi_33)
+                   +1/4 * (lamda*g)^4 (C40 + C42 cos[2(phi-phi_42)] + C44 cos[4(phi-phi_42)]
+                   +1/f * (lamda*g)^f Sum (Cfm cos[m(phi-phi_fm)] where m=[0,2,..f] for even f and m=[1,3,..,f] for odd f-->
+    <!--Thilo Remmele also mentions that there is a mapping of aberration coefficient names:
+C_2_0 -> C1 Defocus
+C_2_2 -> A1 2-fold astigmatism
+C_3_3 -> A2 3-fold astigmatism
+C_3_1 -> B2 axial coma
+C_4_0 -> C3 spherical aberration
+C_4_4 -> A3 4-fold astigmatism
+C_4_2 -> S3 star aberration
+C_5_5 -> A4 5-fold astigmatism-->
+    <!--C_5_1 -> B4 axial coma
+C_5_3 -> D4 three lobe aberration
+C_6_0 -> C5 spherical aberration
+C_6_2 -> S5 star aberration
+C_6_4 -> R5 rosette aberration
+C_6_6 -> A5 6-fold astigmatism-->
+    <!--In a session with HRTEM images the corrector is commonly aligned.
+The final measurement with the estimated residual aberrations
+should be saved in a corrector.html file (an example is appended
+at the end of this file. Unfortunately the datetime is not included
+in that html output, nor is the used outer tilt angle and exposure time.
+The datetime may be estimated from the file datetime and the Delta t entry,
+but caution if that datetime is not preserved on file transfers!
+More than one detector entry could occure but is not common.
+A seperate corrector schema, so it can be easily exchanged to other correctors if necessary.
+It might be useful to collect all the corrector entries in one table, for example to analyse the performance of the corrector.
+The corrector entry of the nexus em definition lacks the confidence information and the
+parameter settings for the estimation oft the aberrations.-->
+</definition>

contributed_definitions/NXaberration_model_nion.nxdl.xml

@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+# 
+# Copyright (C) 2014-2022 NeXus International Advisory Committee (NIAC)
+# 
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# For further information, see http://www.nexusformat.org
+-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" extends="NXobject" name="NXaberration_model_nion" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <doc>
+         NION definitions/model for aberrations of electro-magnetic lenses.
+
+         See `S. J. Pennycock and P. D. Nellist &lt;https://doi.org/10.1007/978-1-4419-7200-2&gt;`_ (page 44ff, and page 118ff)
+         for different definitions available and further details. Table 7-2 of Ibid.
+         publication (page 305ff) documents how to convert from the NION to the 
+         CEOS definitions.
+    </doc>
+    <field name="model">
+        <enumeration>
+            <item value="nion"/>
+        </enumeration>
+    </field>
+    <group name="c_1_0" type="NXaberration"/>
+    <group name="c_1_2_a" type="NXaberration"/>
+    <group name="c_1_2_b" type="NXaberration"/>
+    <group name="c_2_1_a" type="NXaberration"/>
+    <group name="c_2_1_b" type="NXaberration"/>
+    <group name="c_2_3_a" type="NXaberration"/>
+    <group name="c_2_3_b" type="NXaberration"/>
+    <group name="c_3_0" type="NXaberration"/>
+    <group name="c_3_2_a" type="NXaberration"/>
+    <group name="c_3_2_b" type="NXaberration"/>
+    <group name="c_3_4_a" type="NXaberration"/>
+    <group name="c_3_4_b" type="NXaberration"/>
+    <group name="c_4_1_a" type="NXaberration"/>
+    <group name="c_4_1_b" type="NXaberration"/>
+    <group name="c_4_3_a" type="NXaberration"/>
+    <group name="c_4_3_b" type="NXaberration"/>
+    <group name="c_4_5_a" type="NXaberration"/>
+    <group name="c_4_5_b" type="NXaberration"/>
+    <group name="c_5_0" type="NXaberration"/>
+    <group name="c_5_2_a" type="NXaberration"/>
+    <group name="c_5_2_b" type="NXaberration"/>
+    <group name="c_5_4_a" type="NXaberration"/>
+    <group name="c_5_4_b" type="NXaberration"/>
+    <group name="c_5_6_a" type="NXaberration"/>
+    <group name="c_5_6_b" type="NXaberration"/>
+</definition>