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How to define your own sequence to build an NXtomo
==================================================
Design
""""""
The conversion process is done as follow:
.. image:: img/nxtomomill_design_1.png
The first step this can be done two ways
.. image:: img/nxtomomill_design_2.png
Until now we were only using the title to deduce the acquisition and the type of frames of each Bliss entry.
But the `FRAME_TYPE_SECTION` allow us to ignore those titles and define manually the sequence of the acquisition.
Coming back to the `FRAME_TYPE_SECTION` section
`FRAME_TYPE_SECTION` section
''''''''''''''''''''''''''''
If this section is fill then the `ENTRIES_AND_TITLES_SECTION` will be ignored. Those are mutually exclusive sections.
From it we can define `data_scans` that allow us to define a sequence of scan defining an acquisition using [url](https://fr.wikipedia.org/wiki/Uniform_Resource_Locator). Like:
.. code-block:: text
data_scans = (
(frame_type=projections, entry=silx:///path/to/file?/path/to/scan/node,),
(frame_type=projections, entry=/path_relative_to_file),
)
Here we will create one acquisition from `silx:///path/to/file?/path/to/scan/node` to be used as a set of projections and `/path_relative_to_file` as a set of projections to.
.. note::
Url can be relative to different file
.. warning::
The created acquisition will follow the provided order
Example: create an NXtomo using the `data_scans` field
""""""""""""""""""""""""""""""""""""""""""""""""""""""
Using the configuration file
''''''''''''''''''''''''''''
You can find a file `conversion_using_data_scans.cfg` in the `solution` folder that create an acquisition using `data_scans`:
.. image:: img/nxtomomill_example_data_scans.png
It can be executed by calling:
.. code-block:: bash
nxtomomill h52nx --config conversion_using_data_scans.cfg
Using the python API
''''''''''''''''''''
.. code-block:: python
from nxtomomill.converter import from_h5_to_nx
from nxtomomill.io.config import TomoHDF5Config
from nxtomomill.io.config.h52nxtomo_models import FrameGroup
from silx.io.url import DataUrl
input_file_path = "bambou_hercules_0001.h5"
configuration = TomoHDF5Config()
configuration.input_file = input_file_path
configuration.output_file = "bambou_hercules_0001.nx"
configuration.data_scans = (
FrameGroup(
url=DataUrl(
file_path=input_file_path,
data_path="1.1",
scheme="silx",
),
frame_type="initialization",
),
FrameGroup(
url=DataUrl(
file_path=input_file_path,
data_path="2.1",
scheme="silx",
),
frame_type="darks",
),
FrameGroup(
url=DataUrl(
file_path=input_file_path,
data_path="3.1",
scheme="silx",
),
frame_type="flats",
),
FrameGroup(
url=DataUrl(
file_path=input_file_path,
data_path="4.1",
scheme="silx",
),
frame_type="projections",
),
)
res = from_h5_to_nx(configuration=configuration)
.. note::
you will see another way to create an NXtomo from scratch that could be another alternative.
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