From 8ac71f39931b1e92f1fdb38f2dec875da9db080c Mon Sep 17 00:00:00 2001 From: Claude Date: Wed, 28 Oct 2026 13:46:35 +0000 Subject: [PATCH] Install bifti in playground notebooks and playground CI MRzeroCore now depends on bifti, but the playground notebooks install MRzeroCore with --no-deps, so bifti was missing. Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01NHKPBcsb28ED47iXtFJjsC --- .github/workflows/playground_test.yml | 1 + documentation/playground_mr0/Pulseq_zero_TSE_FAopt_SARtask.ipynb | 1 + documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb | 1 + documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb | 1 + documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb | 1 + documentation/playground_mr0/mr0_EPI_2D_seq.ipynb | 1 + documentation/playground_mr0/mr0_FID_seq.ipynb | 1 + documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb | 1 + documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb | 1 + documentation/playground_mr0/mr0_RARE_2D_seq.ipynb | 1 + documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb | 1 + documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb | 1 + documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb | 1 + documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb | 1 + .../playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb | 1 + documentation/playground_mr0/mr0_time_vs_acc_bspBSSFP.ipynb | 1 + documentation/playground_mr0/mr0_upload_seq.ipynb | 1 + documentation/playground_mr0/pulseq_zero_DESC_demo.ipynb | 1 + .../playground_mr0/unsorted/mr0_EPI_2D_with_ORC_seq.ipynb | 1 + 19 files changed, 19 insertions(+) diff --git a/.github/workflows/playground_test.yml b/.github/workflows/playground_test.yml index 6a45c92c..b7972064 100644 --- a/.github/workflows/playground_test.yml +++ b/.github/workflows/playground_test.yml @@ -56,6 +56,7 @@ jobs: pip install pydisseqt pip install ismrmrd pip install MRzeroCore --no-deps + pip install bifti pip install torchkbnufft PyWavelets tqdm scikit-image wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null pip install jupyter nbconvert diff --git a/documentation/playground_mr0/Pulseq_zero_TSE_FAopt_SARtask.ipynb b/documentation/playground_mr0/Pulseq_zero_TSE_FAopt_SARtask.ipynb index f7fa738a..5064ea19 100644 --- a/documentation/playground_mr0/Pulseq_zero_TSE_FAopt_SARtask.ipynb +++ b/documentation/playground_mr0/Pulseq_zero_TSE_FAopt_SARtask.ipynb @@ -80,6 +80,7 @@ "!pip install pulseqzero==0.2.1\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps &> /dev/null\n", + "!pip install bifti --no-deps &> /dev/null\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null\n" diff --git a/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb b/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb index ff8e86d4..da3537aa 100644 --- a/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb +++ b/documentation/playground_mr0/mr0_DREAM_STE_seq.ipynb @@ -29,6 +29,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb b/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb index 1e43eb12..b5a5d099 100644 --- a/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb +++ b/documentation/playground_mr0/mr0_DREAM_STID_seq.ipynb @@ -53,6 +53,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb b/documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb index 683e8a85..7ae6342a 100644 --- a/documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb +++ b/documentation/playground_mr0/mr0_DWI_SE_EPI.ipynb @@ -62,6 +62,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/subject05.npz &> /dev/null" diff --git a/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb b/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb index 44b7073a..536df1d7 100644 --- a/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb +++ b/documentation/playground_mr0/mr0_EPI_2D_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_FID_seq.ipynb b/documentation/playground_mr0/mr0_FID_seq.ipynb index 1f176d63..5fa12621 100644 --- a/documentation/playground_mr0/mr0_FID_seq.ipynb +++ b/documentation/playground_mr0/mr0_FID_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb b/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb index a37c7907..31150f15 100644 --- a/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb +++ b/documentation/playground_mr0/mr0_FLASH_2D_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb b/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb index 53df4ec1..7752a2eb 100644 --- a/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb +++ b/documentation/playground_mr0/mr0_GRE_to_FLASH.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt" ] }, diff --git a/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb b/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb index 7dc1ec76..73286711 100644 --- a/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb +++ b/documentation/playground_mr0/mr0_RARE_2D_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb b/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb index 6f419779..dca23d7c 100644 --- a/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb +++ b/documentation/playground_mr0/mr0_SE_CPMG_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb b/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb index 85af1d11..6b7cd858 100644 --- a/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb +++ b/documentation/playground_mr0/mr0_STE_3pulses_5echoes_seq.ipynb @@ -44,6 +44,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb b/documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb index 58867dd4..1c8ab7da 100644 --- a/documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb +++ b/documentation/playground_mr0/mr0_TSE_2D_multi_shot_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb b/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb index 8fa18ff1..26c4bee2 100644 --- a/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb +++ b/documentation/playground_mr0/mr0_bSSFP_2D_seq.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null\n", diff --git a/documentation/playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb b/documentation/playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb index 70383dd1..e20820b1 100644 --- a/documentation/playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb +++ b/documentation/playground_mr0/mr0_diffusion_prep_STEAM_2D_seq.ipynb @@ -49,6 +49,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/subject05.npz &> /dev/null" ] diff --git a/documentation/playground_mr0/mr0_time_vs_acc_bspBSSFP.ipynb b/documentation/playground_mr0/mr0_time_vs_acc_bspBSSFP.ipynb index 0dede151..00bd9fc8 100644 --- a/documentation/playground_mr0/mr0_time_vs_acc_bspBSSFP.ipynb +++ b/documentation/playground_mr0/mr0_time_vs_acc_bspBSSFP.ipynb @@ -65,6 +65,7 @@ "!pip install torchkbnufft --no-deps\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null\n", diff --git a/documentation/playground_mr0/mr0_upload_seq.ipynb b/documentation/playground_mr0/mr0_upload_seq.ipynb index 944fb99f..e78ea13c 100644 --- a/documentation/playground_mr0/mr0_upload_seq.ipynb +++ b/documentation/playground_mr0/mr0_upload_seq.ipynb @@ -18,6 +18,7 @@ "\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps &> /dev/null\n", + "!pip install bifti --no-deps &> /dev/null\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null" diff --git a/documentation/playground_mr0/pulseq_zero_DESC_demo.ipynb b/documentation/playground_mr0/pulseq_zero_DESC_demo.ipynb index 7d1d4588..8990b5dd 100644 --- a/documentation/playground_mr0/pulseq_zero_DESC_demo.ipynb +++ b/documentation/playground_mr0/pulseq_zero_DESC_demo.ipynb @@ -25,6 +25,7 @@ "!pip install pulseqzero\n", "!pip install ismrmrd\n", "!pip install MRzeroCore --no-deps &> /dev/null\n", + "!pip install bifti --no-deps &> /dev/null\n", "!pip install pydisseqt" ] }, diff --git a/documentation/playground_mr0/unsorted/mr0_EPI_2D_with_ORC_seq.ipynb b/documentation/playground_mr0/unsorted/mr0_EPI_2D_with_ORC_seq.ipynb index 9cfeceb4..100e7b39 100644 --- a/documentation/playground_mr0/unsorted/mr0_EPI_2D_with_ORC_seq.ipynb +++ b/documentation/playground_mr0/unsorted/mr0_EPI_2D_with_ORC_seq.ipynb @@ -52,6 +52,7 @@ "!pip install pypulseq &> /dev/null\n", "!pip install torchkbnufft --no-deps\n", "!pip install MRzeroCore --no-deps\n", + "!pip install bifti --no-deps\n", "!pip install pydisseqt\n", "\n", "!wget https://github.com/MRsources/MRzero-Core/raw/main/documentation/playground_mr0/numerical_brain_cropped.mat &> /dev/null"