Code

Dp sf pap#547

Code

Merged

daniellepace merged 52 commits intomasterbroadinstitute/ml4h:masterfrom dp_sf_papbroadinstitute/ml4h:dp_sf_papCopy head branch name to clipboardJan 12, 2024

+11-14

Commits

Commits on Sep 5, 2023

• use both _1 and _2 segmentations

  lucidtronix

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• use both _1 and _2 segmentations

  lucidtronix

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Commits on Sep 26, 2023

• TEMP: add dice metrics, copied from neuron

  daniellepace

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  21d95bd

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• ENH: Use dice loss and metrics

  daniellepace

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• ENH: Remove kidney label and merge body/background labels

  daniellepace

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  814f68f

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• FIX: Fix bad number of channels

  daniellepace

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• ENH: Use only one channel of the input image

  daniellepace

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• WIP: hacking bottom of U-net

  daniellepace

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• ENH: Add mean and std for normalization

  daniellepace

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• Merge branch 'master' into dp_sf_pap

  daniellepace

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• ENH: Add neurite and voxelmorph to docker

  daniellepace

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• FIX: Use dice loss from neurite

  daniellepace

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Commits on Sep 27, 2023

• STYLE: Fix up WIP code on hacking bottom of U-net

  daniellepace

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Commits on Sep 29, 2023

• ENH: Add merged paps for segmentation tensormap

  daniellepace

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• WIP: Fix Unet concats

  daniellepace

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Commits on Oct 5, 2023

• FIX: Fix soft dice metrics

  daniellepace

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Commits on Oct 6, 2023

• ENH: Add plot_dice to compare

  daniellepace

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Commits on Oct 13, 2023

• ENH: Add median computation for papillary segmentation project

  daniellepace

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• FIX: Fix double plot on one graph

  daniellepace

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• ENH: Allow generator to have empty path, e.g., to test on all images

  daniellepace

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• ENH: Prune list of structures for which we do stats

  daniellepace

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• STYLE: rearranging

  daniellepace

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• WIP: Handle inference without ground truth labels

  daniellepace

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Commits on Oct 16, 2023

• ENH: Remove option for merged paps

  daniellepace

  committed
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Commits on Oct 17, 2023

• FIX: Get all b2s images, instance_2s only

  daniellepace

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  83e5dc6

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• ENH: Add mri dates

  daniellepace

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Commits on Oct 20, 2023

• FIX: Fix normalization with correct padding

  daniellepace

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  e54d4af

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• FIX: Fix soft dice metrics again

  daniellepace

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  ddb9d46

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• COMP: Add option for environment variable for jupyter notebooks

  daniellepace

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  84c5365

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• WIP: data augmentation

  daniellepace

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Commits on Oct 24, 2023

• WIP: Better scatter plots for medians

  daniellepace

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Commits on Oct 25, 2023

• ENH: Report std too

  daniellepace

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• ENH: Improve dice plots for a single model

  daniellepace

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• ENH: Log pearson correlation coefficients

  daniellepace

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Commits on Nov 1, 2023

• STYLE: Adding TODOs to fix tensor_generators

  daniellepace

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• WIP: Add temporary code to save Dice scores

  daniellepace

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  7b0643d

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• WIP: Add temporary code for plotting medians

  daniellepace

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  e92f133

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• STYLE: Clean up code for infer_medians

  daniellepace

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Commits on Nov 3, 2023

• STYLE: Clean up medians code

  daniellepace

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• STYLE: Add command-line args for median computations

  daniellepace

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• ENH: Add percentiles and tsv for dice calculations

  daniellepace

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  ebcaa9c

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• STYLE: Add command-line args for data augmentation

  daniellepace

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Commits on Nov 9, 2023

• ENH: Improve log files for dice compare

  daniellepace

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Commits on Nov 14, 2023

• STYLE: Small edits requested in PR

  daniellepace

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• STYLE: docstring and typehints for plot_dice

  daniellepace

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• STYLE: docstring for infer_statistics_from_segmented_regions

  daniellepace

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• STYLE: Docstring and typehints for augment_using_layers

  daniellepace

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Commits on Dec 8, 2023

• FIX: Fix typo

  daniellepace

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  c64275e

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• FIX: Fix parser for boolean arguments

  daniellepace

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Commits on Jan 12, 2024

• STYLE: Rename _unit_disk(r) to unit_disk(r)

  daniellepace

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• ENH: Remove --no_analyze_ground_truth option

  daniellepace

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• Merge branch 'master' into dp_sf_pap

  daniellepace

  authored
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