From 843c34c0b56abec000df4feb2f3553070f1104fe Mon Sep 17 00:00:00 2001 From: Behrooz <3968947+drbeh@users.noreply.github.com> Date: Fri, 19 Nov 2021 01:07:20 +0000 Subject: [PATCH 1/2] Add tiffile and imagecodes to build option dependencies Signed-off-by: Behrooz <3968947+drbeh@users.noreply.github.com> --- setup.cfg | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/setup.cfg b/setup.cfg index 03ae724657..c58e683b12 100644 --- a/setup.cfg +++ b/setup.cfg @@ -42,6 +42,8 @@ all = psutil cucim>=21.8.2 openslide-python==1.1.2 + tifffile + imagecodecs pandas einops transformers @@ -74,6 +76,10 @@ cucim = cucim>=21.8.2 openslide = openslide-python==1.1.2 +tifffile = + tifffile +imagecodecs = + imagecodecs pandas = pandas einops = From 74e2e13ccb646e38dbe86cb39918102cc5259b64 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Fri, 19 Nov 2021 09:19:33 +0000 Subject: [PATCH 2/2] update optional dep Signed-off-by: Wenqi Li --- docs/requirements.txt | 2 ++ docs/source/installation.md | 5 +++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index e3b7cb6136..ac9c7f38a7 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -23,3 +23,5 @@ einops transformers mlflow tensorboardX +imagecodecs; platform_system == "Linux" +tifffile; platform_system == "Linux" diff --git a/docs/source/installation.md b/docs/source/installation.md index 008ff00e79..c431b3389a 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -174,9 +174,10 @@ Since MONAI v0.2.0, the extras syntax such as `pip install 'monai[nibabel]'` is - The options are ``` -[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, matplotlib, tensorboardX] +[nibabel, skimage, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, matplotlib, tensorboardX, tifffile, imagecodecs] ``` which correspond to `nibabel`, `scikit-image`, `pillow`, `tensorboard`, -`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `matplotlib`, `tensorboardX` respectively. +`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `matplotlib`, `tensorboardX`, +`tifffile`, `imagecodecs`, respectively. - `pip install 'monai[all]'` installs all the optional dependencies.