Skip to content

Commit

Permalink
Working on image and spectrum
Browse files Browse the repository at this point in the history
  • Loading branch information
@atomprobe-tc
atomprobe-tc committed Jan 16, 2025
1 parent e57e8bf commit 821348a
Show file tree
Hide file tree
Showing 2 changed files with 43 additions and 79 deletions.
50 changes: 12 additions & 38 deletions base_classes/NXimage.nxdl.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,31 +21,13 @@
#
# For further information, see http://www.nexusformat.org
-->
<!--
a key challenge is setting constraints, lets explain with contrasting two use cases:
case 1 assuming an image is nothing but a collection of point-wise information without making explicit tiling and discretization information
case 2 assuming that like most frequently assumed we understand an image probing Euclidean space
assuming that we expect that the image is represented using a pixel grid because it was captured
using sensors that are arranged on generator points of a regular tiling.
in the first case, one should not constrain the dimensions for images beyond 1d
because beyond 1d the question of offset and stride comes up i.e. the question which
tiling is used to construct the sensor array
in the second case, one should constrain the dimensions for all dimensions as otherwise
there are no instructions how to arrange the sensors or the pixels for visualizing the image
because the image is not just a bunch of point wise intensities
but if the dimensions are not constrained again images in application definitions will be represented
using different conventions.-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXimage" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<!--for earlier variants see here
https://github.com/FAIRmat-NFDI/nexus_definitions/commit/0682943baaef54d4a6386b5433f9721af6d3d81b
https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
<symbols>
<symbol name="n_img">
<doc>
Number of images in the stack, for stacks the slowest dimension.
</doc>
</symbol>
<!--should we support further dimensions-->
<symbol name="n_k">
<doc>
Number of image points along the slow dimension (k equivalent to z).
Expand Down Expand Up @@ -89,7 +71,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
* `FFTW by M. Frigo and S. G. Johnson &lt;https://www.fftw.org/fftw3_doc/Tutorial.html#Tutorial&gt;`_
* `Intel MKL by the Intel Co. &lt;https://www.intel.com/content/www/us/en/docs/onemkl/developer-reference-c/2024-2/fourier-transform-functions.html&gt;`_
* `cuFFT by the NVidia Co. &lt;https://docs.nvidia.com/cuda/cufft/index.html&gt;`_
* `NFFT by the Chemnitz group &lt;https://www-user.tu-chemnitz.de/~potts/nfft/&gt;`_ for non-equispaced computations
* `NFFT by the TU Chemnitz group &lt;https://www-user.tu-chemnitz.de/~potts/nfft/&gt;`_ for non-equispaced computations

Users are strongly advised to inspect carefully which specific conventions their library uses
to enable storing and modifying the implementation of their code such that the serialized
Expand All @@ -98,10 +80,10 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
It is often the case that several images are combined using processing. In this case,
the number of images which are combined in a collection is not necessarily the same
for each collection. The NXimage base class addresses this logical distinction
through the notation of image_identifier and group_identifier concepts.
That is image_identifier are always counting from offset in increments of one.
through the notation of identifier_image and identifier_group concepts.
That is identifier_image are always counting from offset in increments of one.
as each image is its own entity. By contrast, a group may contain no, or several images.
Consequently, group_identifier are not required to be contiguous.
Consequently, identifier_group are not required to be contiguous.
</doc>
<group type="NXprocess">
<doc>
Expand All @@ -110,7 +92,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
<group name="source" type="NXserialized">
<doc>
Resolvable data artifact (e.g. file) from which all values in the :ref:`NXdata`
instances in this :ref:`NXimage_set` were loaded during parsing.
instances in this :ref:`NXimage` were loaded during parsing.

Possibility to document from which specific other serialized resource as the source
pieces of information were processed when using NeXus as a semantic file format
Expand All @@ -126,10 +108,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
</doc>
</field>
</group>
<!--mode(NX_CHAR):
doc: |
Imaging (data collection) mode of the instrument during acquisition.-->
<field name="detector_identifier" type="NX_CHAR">
<field name="identifier_detector" type="NX_CHAR">
<doc>
Link or name of an :ref:`NXdetector` instance with which the data were
collected.
Expand All @@ -141,11 +120,6 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
</doc>
</group>
</group>
<!--space(NX_CHAR):
doc:
- |
The reference space in which the image set is defined.
enumeration: [real, reciprocal]-->
<group name="image_1d" type="NXdata">
<doc>
One-dimensional image.
Expand Down Expand Up @@ -395,7 +369,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
<dim index="2" value="n_i"/>
</dimensions>
</field>
<field name="group_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_group" type="NX_INT" units="NX_UNITLESS">
<doc>
Group identifier
</doc>
Expand All @@ -408,7 +382,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
</doc>
</attribute>
</field>
<field name="image_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_image" type="NX_INT" units="NX_UNITLESS">
<doc>
Image identifier
</doc>
Expand Down Expand Up @@ -481,7 +455,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
<dim index="3" value="n_i"/>
</dimensions>
</field>
<field name="group_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_group" type="NX_INT" units="NX_UNITLESS">
<doc>
Group identifier
</doc>
Expand All @@ -494,7 +468,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
</doc>
</attribute>
</field>
<field name="image_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_image" type="NX_INT" units="NX_UNITLESS">
<doc>
Image identifier
</doc>
Expand Down Expand Up @@ -584,7 +558,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
<dim index="4" value="n_i"/>
</dimensions>
</field>
<field name="group_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_group" type="NX_INT" units="NX_UNITLESS">
<doc>
Group identifier
</doc>
Expand All @@ -597,7 +571,7 @@ https://en.wikipedia.org/wiki/Euclidean_tilings_by_convex_regular_polygons-->
</doc>
</attribute>
</field>
<field name="image_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_image" type="NX_INT" units="NX_UNITLESS">
<doc>
Image identifier
</doc>
Expand Down
Loading

0 comments on commit 821348a

Please sign in to comment.