PyPI - httomo-backends - Versions diffs - 2.1__tar.gz → 2.1.1__tar.gz - Mend

httomo-backends 2.1tar.gz → 2.1.1tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (107) hide show

{httomo_backends-2.1 → httomo_backends-2.1.1}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: httomo-backends
-Version: 2.1
+Version: 2.1.1
 Summary: Supplementary files for HTTomo backends.
 Author: Garry ODonnell, Jacob Williamson
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml ADDED Viewed

@@ -0,0 +1,13 @@
+- method: save_to_images
+  module_path: httomolib.misc.images
+  parameters:
+    subfolder_name: images
+    axis: auto
+    file_format: tif
+    bits: 8
+    perc_range_min: 0.0
+    perc_range_max: 100.0
+    jpeg_quality: 95
+    glob_stats: ${{statistics.side_outputs.glob_stats}}
+    watermark_vals: null
+    asynchronous: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: data_reducer
+  module_path: httomolib.misc.morph
+  parameters:
+    axis: auto
+    method: mean

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: binary_thresholding
+  module_path: httomolib.misc.segm
+  parameters:
+    val_intensity: 0.1
+    otsu: false
+    foreground: true
+    axis: auto

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: paganin_filter
+  module_path: httomolib.prep.phase
+  parameters:
+    pixel_size: 0.0001
+    dist: 50.0
+    energy: 53.0
+    alpha: 0.001

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: median_filter
+  module_path: httomolibgpu.misc.corr
+  parameters:
+    kernel_size: 3
+    dif: 0.0

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: remove_outlier
+  module_path: httomolibgpu.misc.corr
+  parameters:
+    kernel_size: 3
+    dif: 0.1

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: data_resampler
+  module_path: httomolibgpu.misc.morph
+  parameters:
+    newshape: REQUIRED
+    axis: auto
+    interpolation: linear

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: sino_360_to_180
+  module_path: httomolibgpu.misc.morph
+  parameters:
+    overlap: ${{centering.side_outputs.overlap}}
+    rotation: left

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: rescale_to_int
+  module_path: httomolibgpu.misc.rescale
+  parameters:
+    perc_range_min: 0.0
+    perc_range_max: 100.0
+    bits: 8
+    glob_stats: ${{statistics.side_outputs.glob_stats}}

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: distortion_correction_proj_discorpy
+  module_path: httomolibgpu.prep.alignment
+  parameters:
+    metadata_path: REQUIRED
+    preview: REQUIRED
+    order: 1
+    mode: reflect

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: normalize
+  module_path: httomolibgpu.prep.normalize
+  parameters:
+    cutoff: 10.0
+    minus_log: true
+    nonnegativity: false
+    remove_nans: false

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml ADDED Viewed

@@ -0,0 +1,11 @@
+- method: paganin_filter_savu
+  module_path: httomolibgpu.prep.phase
+  parameters:
+    ratio: 250.0
+    energy: 53.0
+    distance: 1.0
+    resolution: 1.28
+    pad_y: 100
+    pad_x: 100
+    pad_method: edge
+    increment: 0.0

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: paganin_filter_tomopy
+  module_path: httomolibgpu.prep.phase
+  parameters:
+    pixel_size: 0.0001
+    dist: 50.0
+    energy: 53.0
+    alpha: 0.001

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: remove_all_stripe
+  module_path: httomolibgpu.prep.stripe
+  parameters:
+    snr: 3.0
+    la_size: 61
+    sm_size: 21
+    dim: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: remove_stripe_based_sorting
+  module_path: httomolibgpu.prep.stripe
+  parameters:
+    size: 11
+    dim: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml ADDED Viewed

@@ -0,0 +1,4 @@
+- method: remove_stripe_ti
+  module_path: httomolibgpu.prep.stripe
+  parameters:
+    beta: 0.1

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: CGLS
+  module_path: httomolibgpu.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    recon_size: null
+    iterations: 20
+    nonnegativity: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: FBP
+  module_path: httomolibgpu.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    filter_freq_cutoff: 1.1
+    recon_size: null
+    recon_mask_radius: null

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: LPRec
+  module_path: httomolibgpu.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    recon_size: null
+    recon_mask_radius: null

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: SIRT
+  module_path: httomolibgpu.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    recon_size: null
+    iterations: 300
+    nonnegativity: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml ADDED Viewed

@@ -0,0 +1,15 @@
+- method: find_center_360
+  module_path: httomolibgpu.recon.rotation
+  parameters:
+    ind: null
+    win_width: 10
+    side: null
+    denoise: true
+    norm: false
+    use_overlap: false
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation
+    overlap: overlap
+    side: side
+    overlap_position: overlap_position

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml ADDED Viewed

@@ -0,0 +1,10 @@
+- method: find_center_pc
+  module_path: httomolibgpu.recon.rotation
+  parameters:
+    proj1: auto
+    proj2: auto
+    tol: 0.5
+    rotc_guess: null
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation

httomo_backends-2.1.1/httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml ADDED Viewed

@@ -0,0 +1,13 @@
+- method: find_center_vo
+  module_path: httomolibgpu.recon.rotation
+  parameters:
+    ind: null
+    smin: -50
+    smax: 50
+    srad: 6.0
+    step: 0.25
+    ratio: 0.5
+    drop: 20
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/downsample.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: downsample
+  module_path: tomopy.misc.morph
+  parameters:
+    level: 1
+    axis: auto

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/pad.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: pad
+  module_path: tomopy.misc.morph
+  parameters:
+    axis: REQUIRED
+    npad: null
+    mode: constant

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/sino_360_to_180.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: sino_360_to_180
+  module_path: tomopy.misc.morph
+  parameters:
+    overlap: ${{centering.side_outputs.overlap}}
+    rotation: left

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/trim_sinogram.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: trim_sinogram
+  module_path: tomopy.misc.morph
+  parameters:
+    center: REQUIRED
+    x: REQUIRED
+    y: REQUIRED
+    diameter: REQUIRED

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/upsample.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: upsample
+  module_path: tomopy.misc.morph
+  parameters:
+    level: 1
+    axis: auto

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/add_jitter.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: add_jitter
+  module_path: tomopy.prep.alignment
+  parameters:
+    low: 0
+    high: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/add_noise.yaml ADDED Viewed

@@ -0,0 +1,4 @@
+- method: add_noise
+  module_path: tomopy.prep.alignment
+  parameters:
+    ratio: 0.05

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/align_joint.yaml ADDED Viewed

@@ -0,0 +1,16 @@
+- method: align_joint
+  module_path: tomopy.prep.alignment
+  parameters:
+    fdir: ./
+    iters: 10
+    pad: !!python/tuple
+    - 0
+    - 0
+    blur: true
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    algorithm: sirt
+    upsample_factor: 10
+    rin: 0.5
+    rout: 0.8
+    save: false
+    debug: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/align_seq.yaml ADDED Viewed

@@ -0,0 +1,16 @@
+- method: align_seq
+  module_path: tomopy.prep.alignment
+  parameters:
+    fdir: .
+    iters: 10
+    pad: !!python/tuple
+    - 0
+    - 0
+    blur: true
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    algorithm: sirt
+    upsample_factor: 10
+    rin: 0.5
+    rout: 0.8
+    save: false
+    debug: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/blur_edges.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: blur_edges
+  module_path: tomopy.prep.alignment
+  parameters:
+    low: 0
+    high: 0.8

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_proj.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: distortion_correction_proj
+  module_path: tomopy.prep.alignment
+  parameters:
+    xcenter: REQUIRED
+    ycenter: REQUIRED
+    list_fact: REQUIRED

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_sino.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: distortion_correction_sino
+  module_path: tomopy.prep.alignment
+  parameters:
+    ind: REQUIRED
+    xcenter: REQUIRED
+    ycenter: REQUIRED
+    list_fact: REQUIRED

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/scale.yaml ADDED Viewed

@@ -0,0 +1,3 @@
+- method: scale
+  module_path: tomopy.prep.alignment
+  parameters: {}

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/shift_images.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: shift_images
+  module_path: tomopy.prep.alignment
+  parameters:
+    sx: REQUIRED
+    sy: REQUIRED

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/minus_log.yaml ADDED Viewed

@@ -0,0 +1,3 @@
+- method: minus_log
+  module_path: tomopy.prep.normalize
+  parameters: {}

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: normalize
+  module_path: tomopy.prep.normalize
+  parameters:
+    cutoff: null
+    averaging: mean

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_bg.yaml ADDED Viewed

@@ -0,0 +1,4 @@
+- method: normalize_bg
+  module_path: tomopy.prep.normalize
+  parameters:
+    air: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_nf.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: normalize_nf
+  module_path: tomopy.prep.normalize
+  parameters:
+    flat_loc: REQUIRED
+    cutoff: null
+    averaging: mean

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_roi.yaml ADDED Viewed

@@ -0,0 +1,8 @@
+- method: normalize_roi
+  module_path: tomopy.prep.normalize
+  parameters:
+    roi:
+    - 0
+    - 0
+    - 10
+    - 10

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.phase/retrieve_phase.yaml ADDED Viewed

@@ -0,0 +1,8 @@
+- method: retrieve_phase
+  module_path: tomopy.prep.phase
+  parameters:
+    pixel_size: 0.0001
+    dist: 50
+    energy: 20
+    alpha: 0.001
+    pad: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_all_stripe.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: remove_all_stripe
+  module_path: tomopy.prep.stripe
+  parameters:
+    snr: 3
+    la_size: 61
+    sm_size: 21
+    dim: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_dead_stripe.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: remove_dead_stripe
+  module_path: tomopy.prep.stripe
+  parameters:
+    snr: 3
+    size: 51
+    norm: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_large_stripe.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: remove_large_stripe
+  module_path: tomopy.prep.stripe
+  parameters:
+    snr: 3
+    size: 51
+    drop_ratio: 0.1
+    norm: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_filtering.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: remove_stripe_based_filtering
+  module_path: tomopy.prep.stripe
+  parameters:
+    sigma: 3
+    size: null
+    dim: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_fitting.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: remove_stripe_based_fitting
+  module_path: tomopy.prep.stripe
+  parameters:
+    order: 3
+    sigma: !!python/tuple
+    - 5
+    - 20

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_interpolation.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: remove_stripe_based_interpolation
+  module_path: tomopy.prep.stripe
+  parameters:
+    snr: 3
+    size: 31
+    drop_ratio: 0.1
+    norm: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_sorting.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: remove_stripe_based_sorting
+  module_path: tomopy.prep.stripe
+  parameters:
+    size: null
+    dim: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_fw.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: remove_stripe_fw
+  module_path: tomopy.prep.stripe
+  parameters:
+    level: null
+    wname: db5
+    sigma: 2
+    pad: true

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_sf.yaml ADDED Viewed

@@ -0,0 +1,4 @@
+- method: remove_stripe_sf
+  module_path: tomopy.prep.stripe
+  parameters:
+    size: 5

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_ti.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: remove_stripe_ti
+  module_path: tomopy.prep.stripe
+  parameters:
+    nblock: 0
+    alpha: 1.5

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/stripes_detect3d.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: stripes_detect3d
+  module_path: tomopy.prep.stripe
+  parameters:
+    size: 10
+    radius: 3

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/stripes_mask3d.yaml ADDED Viewed

@@ -0,0 +1,9 @@
+- method: stripes_mask3d
+  module_path: tomopy.prep.stripe
+  parameters:
+    weights: REQUIRED
+    threshold: 0.6
+    min_stripe_length: 20
+    min_stripe_depth: 10
+    min_stripe_width: 5
+    sensitivity_perc: 85.0

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.recon.algorithm/recon.yaml ADDED Viewed

@@ -0,0 +1,7 @@
+- method: recon
+  module_path: tomopy.recon.algorithm
+  parameters:
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    sinogram_order: false
+    algorithm: null
+    init_recon: null

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center.yaml ADDED Viewed

@@ -0,0 +1,15 @@
+- method: find_center
+  module_path: tomopy.recon.rotation
+  parameters:
+    ind: null
+    init: null
+    tol: 0.5
+    mask: true
+    ratio: 1.0
+    sinogram_order: false
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation
+    overlap: overlap
+    side: side
+    overlap_position: overlap_position

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center_pc.yaml ADDED Viewed

@@ -0,0 +1,10 @@
+- method: find_center_pc
+  module_path: tomopy.recon.rotation
+  parameters:
+    proj1: auto
+    proj2: auto
+    tol: 0.5
+    rotc_guess: null
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center_vo.yaml ADDED Viewed

@@ -0,0 +1,13 @@
+- method: find_center_vo
+  module_path: tomopy.recon.rotation
+  parameters:
+    ind: null
+    smin: -50
+    smax: 50
+    srad: 6
+    step: 0.25
+    ratio: 0.5
+    drop: 20
+  id: centering
+  side_outputs:
+    cor: centre_of_rotation

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_drift.yaml ADDED Viewed

@@ -0,0 +1,6 @@
+- method: add_drift
+  module_path: tomopy.sim.project
+  parameters:
+    amp: 0.2
+    period: 50
+    mean: 1

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_focal_spot_blur.yaml ADDED Viewed

@@ -0,0 +1,4 @@
+- method: add_focal_spot_blur
+  module_path: tomopy.sim.project
+  parameters:
+    spotsize: REQUIRED

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_gaussian.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: add_gaussian
+  module_path: tomopy.sim.project
+  parameters:
+    mean: 0
+    std: null

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_poisson.yaml ADDED Viewed

@@ -0,0 +1,3 @@
+- method: add_poisson
+  module_path: tomopy.sim.project
+  parameters: {}

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_rings.yaml ADDED Viewed

@@ -0,0 +1,4 @@
+- method: add_rings
+  module_path: tomopy.sim.project
+  parameters:
+    std: 0.05

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_salt_pepper.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: add_salt_pepper
+  module_path: tomopy.sim.project
+  parameters:
+    prob: 0.01
+    val: null

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml ADDED Viewed

@@ -0,0 +1,5 @@
+- method: add_zingers
+  module_path: tomopy.sim.project
+  parameters:
+    f: 0.01
+    sat: 65536

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project.yaml ADDED Viewed

@@ -0,0 +1,8 @@
+- method: project
+  module_path: tomopy.sim.project
+  parameters:
+    obj: REQUIRED
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    emission: true
+    pad: true
+    sinogram_order: false

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project2.yaml ADDED Viewed

@@ -0,0 +1,10 @@
+- method: project2
+  module_path: tomopy.sim.project
+  parameters:
+    objx: REQUIRED
+    objy: REQUIRED
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    emission: true
+    pad: true
+    sinogram_order: false
+    axis: auto

httomo_backends-2.1.1/httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project3.yaml ADDED Viewed

@@ -0,0 +1,11 @@
+- method: project3
+  module_path: tomopy.sim.project
+  parameters:
+    objx: REQUIRED
+    objy: REQUIRED
+    objz: REQUIRED
+    center: ${{centering.side_outputs.centre_of_rotation}}
+    emission: true
+    pad: true
+    sinogram_order: false
+    axis: auto

{httomo_backends-2.1 → httomo_backends-2.1.1}/httomo_backends.egg-info/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: httomo-backends
-Version: 2.1
+Version: 2.1.1
 Summary: Supplementary files for HTTomo backends.
 Author: Garry ODonnell, Jacob Williamson
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Jessica Verschoyle <jessica.verschoyle@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>, scientificsoftware@diamond.ac.uk

httomo_backends-2.1.1/httomo_backends.egg-info/SOURCES.txt ADDED Viewed

@@ -0,0 +1,104 @@
+LICENSE
+README.md
+pyproject.toml
+httomo_backends.egg-info/PKG-INFO
+httomo_backends.egg-info/SOURCES.txt
+httomo_backends.egg-info/dependency_links.txt
+httomo_backends.egg-info/requires.txt
+httomo_backends.egg-info/top_level.txt
+httomo_backends/methods_database/backends/httomolib/httomolib.yaml
+httomo_backends/methods_database/backends/httomolib/httomolib_modules.yaml
+httomo_backends/methods_database/backends/httomolibgpu/__init__.py
+httomo_backends/methods_database/backends/httomolibgpu/httomolibgpu.yaml
+httomo_backends/methods_database/backends/httomolibgpu/httomolibgpu_modules.yaml
+httomo_backends/methods_database/backends/tomopy/__init__.py
+httomo_backends/methods_database/backends/tomopy/tomopy.yaml
+httomo_backends/methods_database/backends/tomopy/tomopy_modules.yaml
+httomo_backends/scripts/__init__.py
+httomo_backends/scripts/yaml_templates_generator.py
+httomo_backends/scripts/yaml_unsupported_tomopy_remove.py
+httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml
+httomo_backends/yaml_templates/httomo/httomo.methods/calculate_stats.yaml
+httomo_backends/yaml_templates/httomo/httomo.methods/save_intermediate_data.yaml
+httomo_backends/yaml_templates/httomolib/httomolib.misc.images/save_to_images.yaml
+httomo_backends/yaml_templates/httomolib/httomolib.misc.morph/data_reducer.yaml
+httomo_backends/yaml_templates/httomolib/httomolib.misc.segm/binary_thresholding.yaml
+httomo_backends/yaml_templates/httomolib/httomolib.prep.phase/paganin_filter.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/median_filter.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.corr/remove_outlier.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/data_resampler.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.morph/sino_360_to_180.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/rescale_to_int.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/distortion_correction_proj_discorpy.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/normalize.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_savu.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.phase/paganin_filter_tomopy.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_all_stripe.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_based_sorting.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/remove_stripe_ti.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/CGLS.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/FBP.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/LPRec.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/SIRT.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_360.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_pc.yaml
+httomo_backends/yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/find_center_vo.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/adjust_range.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/circ_mask.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/gaussian_filter.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter3d.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter_nonfinite.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_nan.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_neg.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier1d.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier3d.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_ring.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/sobel_filter.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/downsample.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/pad.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/sino_360_to_180.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/trim_sinogram.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.misc.morph/upsample.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/add_jitter.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/add_noise.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/align_joint.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/align_seq.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/blur_edges.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_proj.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/distortion_correction_sino.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/scale.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.alignment/shift_images.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/minus_log.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_bg.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_nf.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.normalize/normalize_roi.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.phase/retrieve_phase.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_all_stripe.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_dead_stripe.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_large_stripe.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_filtering.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_fitting.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_interpolation.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_based_sorting.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_fw.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_sf.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/remove_stripe_ti.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/stripes_detect3d.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.prep.stripe/stripes_mask3d.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.recon.algorithm/recon.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center_pc.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.recon.rotation/find_center_vo.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_drift.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_focal_spot_blur.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_gaussian.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_poisson.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_rings.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_salt_pepper.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/add_zingers.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project2.yaml
+httomo_backends/yaml_templates/tomopy/tomopy.sim.project/project3.yaml

{httomo_backends-2.1 → httomo_backends-2.1.1}/pyproject.toml RENAMED Viewed

@@ -6,8 +6,9 @@ build-backend = "setuptools.build_meta"
 include-package-data = true
 packages = ["httomo_backends",
             "httomo_backends.scripts",
-            "httomo_backends.methods_database",
-            "httomo_backends.yaml_templates",
+            "httomo_backends.methods_database.backends.httomolibgpu",
+            "httomo_backends.methods_database.backends.httomolib",
+            "httomo_backends.methods_database.backends.tomopy",
             ]
 [tool.setuptools.package-data]
@@ -18,6 +19,27 @@ httomo_backends = [
     "yaml_templates/httomo/httomo.data.hdf.loaders/*.yaml",
     "yaml_templates/httomo/httomo.methods/*.yaml",
     "yaml_templates/tomopy/tomopy.misc.corr/*.yaml",
+    "yaml_templates/tomopy/tomopy.misc.morph/*.yaml",
+    "yaml_templates/tomopy/tomopy.prep.alignment/*.yaml",
+    "yaml_templates/tomopy/tomopy.prep.normalize/*.yaml",
+    "yaml_templates/tomopy/tomopy.prep.phase/*.yaml",
+    "yaml_templates/tomopy/tomopy.prep.stripe/*.yaml",
+    "yaml_templates/tomopy/tomopy.recon.algorithm/*.yaml",
+    "yaml_templates/tomopy/tomopy.recon.rotation/*.yaml",
+    "yaml_templates/tomopy/tomopy.sim.project/*.yaml",
+    "yaml_templates/httomolib/httomolib.misc.morph/*.yaml",
+    "yaml_templates/httomolib/httomolib.misc.images/*.yaml",
+    "yaml_templates/httomolib/httomolib.misc.segm/*.yaml",
+    "yaml_templates/httomolib/httomolib.prep.phase/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.misc.corr/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.misc.morph/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.misc.rescale/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.prep.alignment/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.prep.normalize/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.prep.phase/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.prep.stripe/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.recon.algorithm/*.yaml",
+    "yaml_templates/httomolibgpu/httomolibgpu.recon.rotation/*.yaml",
 ]
 [tool.setuptools-git-versioning]
@@ -27,7 +49,7 @@ dev_template = "{tag}"
 [project]
 name = "httomo-backends"
-version = "2.1"
+version = "2.1.1"
 description = "Supplementary files for HTTomo backends."
 readme = "README.md"
 license = {text = "BSD-3-Clause"}

httomo_backends-2.1/httomo_backends.egg-info/SOURCES.txt DELETED Viewed

@@ -1,35 +0,0 @@
-LICENSE
-README.md
-pyproject.toml
-httomo_backends.egg-info/PKG-INFO
-httomo_backends.egg-info/SOURCES.txt
-httomo_backends.egg-info/dependency_links.txt
-httomo_backends.egg-info/requires.txt
-httomo_backends.egg-info/top_level.txt
-httomo_backends/methods_database/__init__.py
-httomo_backends/methods_database/backends/httomolib/httomolib.yaml
-httomo_backends/methods_database/backends/httomolib/httomolib_modules.yaml
-httomo_backends/methods_database/backends/httomolibgpu/httomolibgpu.yaml
-httomo_backends/methods_database/backends/httomolibgpu/httomolibgpu_modules.yaml
-httomo_backends/methods_database/backends/tomopy/tomopy.yaml
-httomo_backends/methods_database/backends/tomopy/tomopy_modules.yaml
-httomo_backends/scripts/__init__.py
-httomo_backends/scripts/yaml_templates_generator.py
-httomo_backends/scripts/yaml_unsupported_tomopy_remove.py
-httomo_backends/yaml_templates/__init__.py
-httomo_backends/yaml_templates/httomo/httomo.data.hdf.loaders/standard_tomo.yaml
-httomo_backends/yaml_templates/httomo/httomo.methods/calculate_stats.yaml
-httomo_backends/yaml_templates/httomo/httomo.methods/save_intermediate_data.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/adjust_range.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/circ_mask.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/gaussian_filter.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter3d.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/median_filter_nonfinite.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_nan.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_neg.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier1d.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_outlier3d.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/remove_ring.yaml
-httomo_backends/yaml_templates/tomopy/tomopy.misc.corr/sobel_filter.yaml