diff --git a/.gitignore b/.gitignore index d40b4a5df..33a03d0ed 100644 --- a/.gitignore +++ b/.gitignore @@ -25,6 +25,7 @@ testing/config_segmentation_temp.yaml testing/failures.log coverage.xml mlcube/workspace/* +!.spelling/.spelling/expect.txt !mlcube/workspace/config.yml !mlcube/workspace/channelIDs.yml tutorials/classification_medmnist_notebook/dataset/pathmnist diff --git a/.spelling/.spelling/expect.txt b/.spelling/.spelling/expect.txt new file mode 100644 index 000000000..795ac46eb --- /dev/null +++ b/.spelling/.spelling/expect.txt @@ -0,0 +1,726 @@ +Abhishek +Abousamra +acdfbac +acsconv +adadelta +adagrad +adamax +adamw +addcdiv +addcmul +addgroup +addoption +ademamix +agc +agni +Aimilia +aimiliag +albumentations +allclose +allcontributors +allsigned +amsgrad +Anirban +anonymization +applyaugs +apptainer +Aqubvel +arange +archs +arcname +argmax +argwhere +Arnout +arxiv +asarray +astype +atleast +augs +auroc +autobuild +autocast +autodetermined +auxilary +avgs +awaa +Babak +bacf +backprop +backpropagate +backpropagation +Baheti +Baid +Bakas +Bashyam +batchnorm +bdfc +beggining +bgr +Bhalerao +bibtex +bincount +biomedicalimaging +Bjoern +blabla +brahim +brainage +Brox +btw +Buildx +BVd +BVpye +capsys +cbica +cbig +cca +CCE +cdc +cdir +cel +cencoder +centercrop +cff +Chitalia +christos +Chunrui +Chv +cla +classif +classitk +codacy +codecov +CODEOWNERS +codeql +codereview +codespace +Colab +colorconv +colorjitter +colorlog +commandline +configfile +configgenerator +convs +cooldown +cosineannealing +cosineannealinglr +cosinesimilarity +croporpad +cropzero +ctc +CUBLAS +cudnn +cycliclr +datacenter +dataframe +dataprep +datestampnow +Davatzikos +dcce +dclog +dcm +dcmtk +deac +deadsnakes +DEBIAN +deconv +deepresunet +Deepthi +deepunet +denseblock +denselayer +densenet +depthconv +Despina +despinak +devcontainer +dfu +dicelog +dicom +dicomanonymizer +digestpath +disaggregating +discussioncomment +distilbert +DLF +DNN +dockerfiles +dockerized +dockertag +doi 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+JBHI +JDu +JSTARS +Junwen +jupyter +Jupyterlab +kaiming +kakumarabhishek +Karargyris +Karkada +keepdim +keleshev +kenshohara +KFold +kickstart +kld +Kontos +ksel +kspace +Kullback +Kurc +labelsample +labelsampler +lambd +layerchange +Lbtnaq +ldir +leakyrelu +Leibler +levelname +levelno +libgl +libjpeg +libpython +libsm +libvips +libxext +lightresunet +lightunet +linalg +linenums +lineplot +linspace +linting +lly +logit +logpt +logsoftmax +logvar +longreprtext +lps +lrelu +LROn +lstsq +lucidrains +macenko +mainrun +makereport +mathews +matplotlib +matthews +maxpool +mbergman +mcc +mcclog +MCD +mcr +MCT +mde +mdmc +medcam +medmnist +medperf +medpy +Megh +mencoder +menze +metr +miccai +missingprediction +mkdocs +mlco +mlcommons +mlcube +mlcubedir +mlp +modeified +modelbase +modelcard +modeldir +modelio +monai +Mouchtaris +moveaxis +mpp +mps +mri +msa +mscadocs +msdnet +mse +msle +Mukhopadhyay +multiclass +multidim +multilabel +mytagname +nadam +nans +naveenk +ncbi +ncc +ndarray +ndexbio 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+residualunet +resnet +resunet +rgbatorgb +rgbtorgba +rigourous +Ritesh +rmsprop +rocm +rocmdocs +Ronneberger +rowvar +ruifrok +runnning +runtest +Saltz +samplewise +Sarthak +sarthakpati +savefig +sbakas +sbia +scikit +scipy +screenshots +scse +sdata +sdnet +seaborn +Seac +sebastianffx +securefederatedai +segmap +segmask +segmentor +Sens +sessionstart +setbiasranges +setcutoffrange +setsigmaranges +Sezgin +sge +Shahira +shubham +siddhesh +sigstore +silu +Simonyan +simpleitk +sitk +skimage +sklearn +slurm +smi +socio +Soham +Sotirios +sparseadam +spellchecker +Sprop +Spyridon +ssim +stackexchange +stainextract +stainlib +steplr +stepsize +subjectid +sume +superfences +sustainability +swapaxes +Tahsin +tcia +tempconvs +tensorboard +tgz +thresholded +thresholding +Thu +tiatoolbox +tiffslide +timepoints +timm +tio +tioq +tiosd +TLDR +tmi +TOOLSDIRECTORY +torchaudio +torchinfo +torchio +torchmetrics +torchvision +towardsdatascience +TPAMI +tqdm +traininginference +transunet +triaged +tryfirst +tsaftaris +TUDA +tversky +uanced +uinc +Ujjwal +Umeton +unet +unetr +uniformsample +uniformsampler +unittests +unitwise +unsqueeze +upenn +Uploaing +Uploded +upsample +upsampled +upsampling +utm +uzh +vahadane +validing +valuetopredict +vgg +Vinayak +vios +visualstudiomagazine +vmem +voxel +VRAM +vtk +vvv +WACV +warmupcosineschedule +Wauplin +wcs +weightedsample +weightedsampler +whl +WORKDIR +wsi +wsl +xavier +xdim +XDl +XEI +xkq +xlabel +xlim +xnat +XResolution +XTools +yamlchecker +yamlvalidator +ydim +ylabel +YResolution +Yrv +Yuemeng +zarr +Zeroplanes +zicat +znorm +ZNormalization +Zou +abebbed +adipocytes +afcc +AMNIST +autorefs +avq +baf +bdf +bfa +bjoh +cadf +cbcb +cdbe +cividis +cmap +CMNIST +colorectal +colormaps +cxbdfkig +dbdf +Deconvolutional +Dermatoscope +dff +eaik +edc +eeaf +eee +enu +faa +fdb +fdc +hdwlu +hjzwmjxvamrxotxu +ifqqtrs +ihd +Ingnore +ipykernel +ipynb +ipynbcheckpoints +jjzoifpdly +Kather +kernelspec +Krisam +lexer +lkrvyj +luap +mkdocstrings +MNIST +mpimg +mtdpzx +nbconvert +nbformat +nhfspc +ocflopa +OCTMNIST +pmkdaguy +pvqg +qfzk +qwuvqx +redownload +rsmff +rxtzgrcaq +SMNIST +swp +torchtext +uzbklab +uzsc +viridis +xaburhd +xso +ystore +Zisserman +zsuokb +zwezggl +zzokqk \ No newline at end of file diff --git a/GANDLF/cli/huggingface_hub_handler.py b/GANDLF/cli/huggingface_hub_handler.py index 72e2f35b0..b09fa9743 100644 --- a/GANDLF/cli/huggingface_hub_handler.py +++ b/GANDLF/cli/huggingface_hub_handler.py @@ -121,7 +121,7 @@ def push_to_model_hub( ignore_patterns=ignore_patterns, delete_patterns=delete_patterns, ) - print("Model Sucessfully Uploded") + print("Model Successfully Uploded") def download_from_hub( diff --git a/GANDLF/compute/forward_pass.py b/GANDLF/compute/forward_pass.py index 69efa15a9..2135ca0ee 100644 --- a/GANDLF/compute/forward_pass.py +++ b/GANDLF/compute/forward_pass.py @@ -89,7 +89,7 @@ def validate_network( # # putting stuff in individual arrays for correlation analysis # all_targets = [] - # all_predics = [] + # all_predicts = [] if params["medcam_enabled"] and params["model"]["type"] == "torch": model.enable_medcam() params["medcam_enabled"] = True diff --git a/GANDLF/compute/step.py b/GANDLF/compute/step.py index 148d206cf..1d9db8c12 100644 --- a/GANDLF/compute/step.py +++ b/GANDLF/compute/step.py @@ -98,7 +98,7 @@ def step( f"Model output is not a Tensor: {type(output)}. Say, `deep_resunet` and `deep_unet` may return " f"list of tensors on different scales instead of just one prediction Tensor. However due to " f"GaNDLF architecture it is expected that models return only one tensor. For deep_* models " - f"only the biggeest scale is processed. Use these models with caution till fix is implemented." + f"only the biggest scale is processed. Use these models with caution till fix is implemented." ) output = output[0] diff --git a/GANDLF/data/patch_miner/opm/utils.py b/GANDLF/data/patch_miner/opm/utils.py index 1bee9b1f1..ed2e57258 100644 --- a/GANDLF/data/patch_miner/opm/utils.py +++ b/GANDLF/data/patch_miner/opm/utils.py @@ -431,7 +431,7 @@ def generate_initial_mask(slide_path: str, scale: int) -> Tuple[np.ndarray, tupl slide = tiffslide.open_slide(slide_path) slide_dims = slide.dimensions - # Call thumbnail for effiency, calculate scale relative to whole slide + # Call thumbnail for efficiency, calculate scale relative to whole slide slide_thumbnail = np.asarray( slide.get_thumbnail((slide_dims[0] // scale, slide_dims[1] // scale)) ) diff --git a/GANDLF/metrics/segmentation.py b/GANDLF/metrics/segmentation.py index 82254079f..cd1a7637b 100644 --- a/GANDLF/metrics/segmentation.py +++ b/GANDLF/metrics/segmentation.py @@ -226,7 +226,7 @@ def _calculator_sensitivity_specificity( float, float: The sensitivity and specificity between the object(s) in ```inp``` and the object(s) in ```target```. """ # inMask is mask of input array equal to a certain tissue (ie. all one's in tumor core) - # Ref mask is mask of certain tissue in ground truth (ie. all one's in refernce core ) + # Ref mask is mask of certain tissue in ground truth (ie. all one's in reference core ) # overlap is mask where the two equal each other # They are of the total number of voxels of the ground truth brain mask diff --git a/docs/extending.md b/docs/extending.md index 929efa515..897bf1e9b 100644 --- a/docs/extending.md +++ b/docs/extending.md @@ -80,7 +80,7 @@ To update/change/add a dependency in [setup](https://github.com/mlcommons/GaNDLF ## Adding new CLI command Example: `gandlf config-generator` [CLI command](https://github.com/mlcommons/GaNDLF/blob/master/GANDLF/entrypoints/config_generator.py) - Implement function and wrap it with `@click.command()` + `@click.option()` -- Add it to `cli_subommands` [dict](https://github.com/mlcommons/GaNDLF/blob/master/GANDLF/entrypoints/subcommands.py) +- Add it to `cli_subcommands` [dict](https://github.com/mlcommons/GaNDLF/blob/master/GANDLF/entrypoints/subcommands.py) The command would be available under `gandlf your-subcommand-name` CLI command. ## Update parameters diff --git a/docs/usage.md b/docs/usage.md index 1f56947c9..24738d056 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -603,7 +603,7 @@ To upload to a dataset or a Space, use the --repo-type option: ### Huggingface Template For Upload #### Design and Modify Template -To design the huggingface template use the hugging_face.md file change the medatory field +To design the huggingface template use the hugging_face.md file change the mandatory field [REQUIRED_FOR_GANDLF] to it's respective name don't leave it blank other wise it may through error, other field can be modeified by the user as per his convenience ```bash diff --git a/testing/test_full.py b/testing/test_full.py index 50b628e76..eccf0b3c8 100644 --- a/testing/test_full.py +++ b/testing/test_full.py @@ -2110,7 +2110,7 @@ def test_generic_one_hot_logic(): def test_generic_anonymizer(): - print("33: Starting anomymizer tests") + print("33: Starting anonymizer tests") input_file = get_testdata_file("MR_small.dcm") output_file = os.path.join(outputDir, "MR_small_anonymized.dcm") @@ -3292,14 +3292,14 @@ def test_generic_logging(capsys): os.remove(log_file) - # test the stout info level. The stout must show only INFO messages - message = "Testing stout logging" + # test the stdout info level. The stdout must show only INFO messages + message = "Testing stdout logging" logging.info(message) capture = capsys.readouterr() assert message in capture.out - # Test the stout not showing other messages - message = "Testing stout logging" + # Test the stdout not showing other messages + message = "Testing stdout logging" logging.debug(message) logging.warning(message) logging.error(message) @@ -3307,14 +3307,14 @@ def test_generic_logging(capsys): capture = capsys.readouterr() assert message not in capture.out - # test sterr must NOT show these messages. - message = "Testing sterr logging" + # test stderr must NOT show these messages. + message = "Testing stderr logging" logging.info(message) logging.debug(message) capture = capsys.readouterr() assert message not in capture.err - # test sterr must show these messages. + # test stderr must show these messages. logging.error(message) logging.warning(message) logging.critical(message)