Commit 803502a4 authored by Pierre Paleo's avatar Pierre Paleo
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nabu.preproc.double\_flat\_field module nabu.preproc.double\_flatfield module
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.. automodule:: nabu.preproc.double_flat_field .. automodule:: nabu.preproc.double_flatfield
:members: :members:
:undoc-members: :undoc-members:
:show-inheritance: :show-inheritance:
nabu.preproc.double\_flatfield\_cuda module
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.. automodule:: nabu.preproc.double_flatfield_cuda
:members:
:undoc-members:
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...@@ -10,7 +10,8 @@ Submodules ...@@ -10,7 +10,8 @@ Submodules
nabu.preproc.alignment nabu.preproc.alignment
nabu.preproc.ccd nabu.preproc.ccd
nabu.preproc.ccd_cuda nabu.preproc.ccd_cuda
nabu.preproc.double_flat_field nabu.preproc.double_flatfield
nabu.preproc.double_flatfield_cuda
nabu.preproc.phase nabu.preproc.phase
nabu.preproc.phase_cuda nabu.preproc.phase_cuda
nabu.preproc.rings nabu.preproc.rings
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...@@ -29,19 +29,19 @@ API: [CCDCorrection](apidoc/nabu.preproc.ccd.rst#nabu.preproc.ccd.CCDCorrection) ...@@ -29,19 +29,19 @@ API: [CCDCorrection](apidoc/nabu.preproc.ccd.rst#nabu.preproc.ccd.CCDCorrection)
### Double flat-field ### Double flat-field
This is a projections-based rings artefacts removal. This is a projections-based rings artefacts removal.
Some defects might remain in the projections even after flat-fielding. These defects are visible as structured noise in the projections or sinograms. Some defects might remain in the projections even after flat-fielding. These defects are visible as structured noise in the projections or sinograms.
By doing the average of all projections, the genuine features are canceled out and only the defects remain. This "average image" is used to remove the defects from the radios. Schematically, this method does `radio = radio / mean(radios)` (or other operations if the logarithm of radios was already taken). By doing the average of all projections, the genuine features are canceled out and only the defects remain. This "average image" is used to remove the defects from the radios. Schematically, this method does `radio = radio / mean(radios)` (or other operations if the logarithm of radios was already taken).
Be aware that by doing so, you might lose the quantitativeness of the reconstructed data. Be aware that by doing so, you might lose the quantitativeness of the reconstructed data.
This method assumes that when averaging all the radios, the genuine feature will cancel and only spurious artefacts will remain. This assumption can fail if genuine features are (more or less) independent from the projection angle, ex. ring-shaped. This method assumes that when averaging all the radios, the genuine feature will cancel and only spurious artefacts will remain. This assumption can fail if genuine features are (more or less) independent from the projection angle, ex. ring-shaped.
Configuration file key: section `[preproc]`: `double_flatfield_enabled = 1`. Configuration file key: section `[preproc]`: `double_flatfield_enabled = 1`.
API: [DoubleFlatField](apidoc/nabu.preproc.double_flat_field.rst#nabu.preproc.double_flat_field.DoubleFlatField) API: [DoubleFlatField](apidoc/nabu.preproc.double_flatfield.rst#nabu.preproc.double_flatfield.DoubleFlatField) and [CudaDoubleFlatField](apidoc/nabu.preproc.double_flatfield_cuda.rst#nabu.preproc.double_flatfield_cuda.CudaDoubleFlatField)
### Logarithm ### Logarithm
...@@ -67,7 +67,7 @@ See also: [Phase retrieval](phase.md) ...@@ -67,7 +67,7 @@ See also: [Phase retrieval](phase.md)
### Paganin phase retrieval ### Paganin phase retrieval
The Paganin method consists in applying a band-pass filter on the radios. The Paganin method consists in applying a band-pass filter on the radios.
It depends on the δ/β ratio (assumed to be constant in all the image) and the incoming beam energy. It depends on the δ/β ratio (assumed to be constant in all the image) and the incoming beam energy.
Configuration file: section `[phase]`: `method = Paganin`, `delta_beta = 1000.0` Configuration file: section `[phase]`: `method = Paganin`, `delta_beta = 1000.0`
...@@ -88,7 +88,7 @@ Setting `coeff` to zero (default) disables unsharp masking. ...@@ -88,7 +88,7 @@ Setting `coeff` to zero (default) disables unsharp masking.
Tomographic reconstruction is the process of reconstructing the volume from projections/sinograms. Tomographic reconstruction is the process of reconstructing the volume from projections/sinograms.
Configuration file: section `[reconstruction]`. Configuration file: section `[reconstruction]`.
Related keys: `angles_file`, `angle_offset`, `rotation_axis_position`, `enable_halftomo` Related keys: `angles_file`, `angle_offset`, `rotation_axis_position`, `enable_halftomo`
`start_x`, `end_x`, `start_y`, `end_y`, `start_z`, `end_z`. `start_x`, `end_x`, `start_y`, `end_y`, `start_z`, `end_z`.
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