Merge pull request #20 from andreped/dev

Added linting + filesize workflows; linting checks; removed old demo

.github/workflows/filesize.yml

@@ -0,0 +1,16 @@
+name: Check file size
+on:               # or directly `on: [push]` to run the action on every push on any branch
+  pull_request:
+    branches: [ main ]
+
+  # to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  check-filesize:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check large files
+        uses: ActionsDesk/lfs-warning@v2.0
+        with:
+          filesizelimit: 10485760 # this is 10MB so we can sync to HF Spaces

.github/workflows/linting.yml

@@ -0,0 +1,26 @@
+name: Linting
+
+on:
+  push:
+    branches:
+      - '*'
+  pull_request:
+    branches:
+      - '*'
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      
+      - name: Install lint dependencies
+        run: pip install wheel setuptools black==22.3.0 isort==5.10.1 flake8==4.0.1
+
+      - name: Lint the code
+        run: sh shell/lint.sh

AeroPath/gui.py

@@ -1,171 +0,0 @@
-import os
-
-import gradio as gr
-
-from .inference import run_model
-from .utils import load_ct_to_numpy
-from .utils import load_pred_volume_to_numpy
-from .utils import nifti_to_glb
-
-
-class WebUI:
-    def __init__(
-        self,
-        model_name: str = None,
-        cwd: str = "/home/user/app/",
-        share: int = 1,
-    ):
-        # global states
-        self.images = []
-        self.pred_images = []
-
-        # @TODO: This should be dynamically set based on chosen volume size
-        self.nb_slider_items = 415
-
-        self.model_name = model_name
-        self.cwd = cwd
-        self.share = share
-
-        self.class_name = "airways"  # default
-        self.class_names = {
-            "airways": "CT_Airways",
-            "lungs": "CT_Lungs",
-        }
-
-        self.result_names = {
-            "airways": "Airways",
-            "lungs": "Lungs",
-        }
-
-        # define widgets not to be rendered immediately, but later on
-        self.slider = gr.Slider(
-            1,
-            self.nb_slider_items,
-            value=1,
-            step=1,
-            label="Which 2D slice to show",
-        )
-        self.volume_renderer = gr.Model3D(
-            clear_color=[0.0, 0.0, 0.0, 0.0],
-            label="3D Model",
-            visible=True,
-            elem_id="model-3d",
-        ).style(height=512)
-
-    def set_class_name(self, value):
-        print("Changed task to:", value)
-        self.class_name = value
-
-    def combine_ct_and_seg(self, img, pred):
-        return (img, [(pred, self.class_name)])
-
-    def upload_file(self, file):
-        return file.name
-
-    def process(self, mesh_file_name):
-        path = mesh_file_name.name
-        run_model(
-            path,
-            model_path=os.path.join(self.cwd, "resources/models/"),
-            task=self.class_names[self.class_name],
-            name=self.result_names[self.class_name],
-        )
-        nifti_to_glb("prediction.nii.gz")
-
-        self.images = load_ct_to_numpy(path)
-        self.pred_images = load_pred_volume_to_numpy("./prediction.nii.gz")
-        return "./prediction.obj"
-
-    def get_img_pred_pair(self, k):
-        k = int(k) - 1
-        out = [gr.AnnotatedImage.update(visible=False)] * self.nb_slider_items
-        out[k] = gr.AnnotatedImage.update(
-            self.combine_ct_and_seg(self.images[k], self.pred_images[k]),
-            visible=True,
-        )
-        return out
-
-    def run(self):
-        css = """
-        #model-3d {
-        height: 512px;
-        }
-        #model-2d {
-        height: 512px;
-        margin: auto;
-        }
-        #upload {
-        height: 120px;
-        }
-        """
-        with gr.Blocks(css=css) as demo:
-            with gr.Row():
-                file_output = gr.File(file_count="single", elem_id="upload")
-                file_output.upload(self.upload_file, file_output, file_output)
-
-                model_selector = gr.Dropdown(
-                    list(self.class_names.keys()),
-                    label="Task",
-                    info="Which task to perform - one model for"
-                    "airways and lungs extraction",
-                    multiselect=False,
-                    size="sm",
-                )
-                model_selector.input(
-                    fn=lambda x: self.set_class_name(x),
-                    inputs=model_selector,
-                    outputs=None,
-                )
-
-                run_btn = gr.Button("Run analysis").style(
-                    full_width=False, size="lg"
-                )
-                run_btn.click(
-                    fn=lambda x: self.process(x),
-                    inputs=file_output,
-                    outputs=self.volume_renderer,
-                )
-
-            with gr.Row():
-                gr.Examples(
-                    examples=[
-                        os.path.join(self.cwd, "test_thorax_CT_ds.nii"),
-                        os.path.join(self.cwd, "test_thorax_CT_ds.nii"),
-                    ],
-                    inputs=file_output,
-                    outputs=file_output,
-                    fn=self.upload_file,
-                    cache_examples=True,
-                )
-
-            with gr.Row():
-                with gr.Box():
-                    with gr.Column():
-                        image_boxes = []
-                        for i in range(self.nb_slider_items):
-                            visibility = True if i == 1 else False
-                            t = gr.AnnotatedImage(
-                                visible=visibility, elem_id="model-2d"
-                            ).style(
-                                color_map={self.class_name: "#ffae00"},
-                                height=512,
-                                width=512,
-                            )
-                            image_boxes.append(t)
-
-                        self.slider.input(
-                            self.get_img_pred_pair, self.slider, image_boxes
-                        )
-
-                        self.slider.render()
-
-                with gr.Box():
-                    self.volume_renderer.render()
-
-        # sharing app publicly -> share=True:
-        # https://gradio.app/sharing-your-app/
-        # inference times > 60 seconds -> need queue():
-        # https://github.com/tloen/alpaca-lora/issues/60#issuecomment-1510006062
-        demo.queue().launch(
-            server_name="0.0.0.0", server_port=7860, share=self.share
-        )

AeroPath/inference.py

@@ -1,103 +0,0 @@
-import configparser
-import logging
-import os
-import shutil
-import traceback
-
-
-def run_model(
-    input_path: str,
-    model_path: str,
-    verbose: str = "info",
-    task: str = "CT_Airways",
-    name: str = "Airways",
-):
-    logging.basicConfig()
-    logging.getLogger().setLevel(logging.WARNING)
-
-    if verbose == "debug":
-        logging.getLogger().setLevel(logging.DEBUG)
-    elif verbose == "info":
-        logging.getLogger().setLevel(logging.INFO)
-    elif verbose == "error":
-        logging.getLogger().setLevel(logging.ERROR)
-    else:
-        raise ValueError("Unsupported verbose value provided:", verbose)
-
-    # delete patient/result folder if they exist
-    if os.path.exists("./patient/"):
-        shutil.rmtree("./patient/")
-    if os.path.exists("./result/"):
-        shutil.rmtree("./result/")
-
-    patient_directory = ''
-    output_path = ''
-    try:
-        # setup temporary patient directory
-        filename = input_path.split("/")[-1]
-        splits = filename.split(".")
-        extension = ".".join(splits[1:])
-        patient_directory = "./patient/"
-        os.makedirs(patient_directory + "T0/", exist_ok=True)
-        shutil.copy(
-            input_path,
-            patient_directory + "T0/" + splits[0] + "-t1gd." + extension,
-        )
-
-        # define output directory to save results
-        output_path = "./result/prediction-" + splits[0] + "/"
-        os.makedirs(output_path, exist_ok=True)
-
-        # Setting up the configuration file
-        rads_config = configparser.ConfigParser()
-        rads_config.add_section("Default")
-        rads_config.set("Default", "task", "mediastinum_diagnosis")
-        rads_config.set("Default", "caller", "")
-        rads_config.add_section("System")
-        rads_config.set("System", "gpu_id", "-1")
-        rads_config.set("System", "input_folder", patient_directory)
-        rads_config.set("System", "output_folder", output_path)
-        rads_config.set("System", "model_folder", model_path)
-        rads_config.set(
-            "System",
-            "pipeline_filename",
-            os.path.join(model_path, task, "pipeline.json"),
-        )
-        rads_config.add_section("Runtime")
-        rads_config.set(
-            "Runtime", "reconstruction_method", "thresholding"
-        )  # thresholding, probabilities
-        rads_config.set("Runtime", "reconstruction_order", "resample_first")
-        rads_config.set("Runtime", "use_preprocessed_data", "False")
-
-        with open("rads_config.ini", "w") as f:
-            rads_config.write(f)
-
-        # finally, run inference
-        from raidionicsrads.compute import run_rads
-
-        run_rads(config_filename="rads_config.ini")
-
-        # rename and move final result
-        os.rename(
-            "./result/prediction-"
-            + splits[0]
-            + "/T0/"
-            + splits[0]
-            + "-t1gd_annotation-"
-            + name
-            + ".nii.gz",
-            "./prediction.nii.gz",
-        )
-        # Clean-up
-        if os.path.exists(patient_directory):
-            shutil.rmtree(patient_directory)
-        if os.path.exists(output_path):
-            shutil.rmtree(output_path)
-    except Exception as e:
-        print(traceback.format_exc())
-        # Clean-up
-        if os.path.exists(patient_directory):
-            shutil.rmtree(patient_directory)
-        if os.path.exists(output_path):
-            shutil.rmtree(output_path)

AeroPath/utils.py

@@ -1,67 +0,0 @@
-import nibabel as nib
-import numpy as np
-from nibabel.processing import resample_to_output
-from skimage.measure import marching_cubes
-
-
-def load_ct_to_numpy(data_path):
-    if type(data_path) != str:
-        data_path = data_path.name
-
-    image = nib.load(data_path)
-    resampled = resample_to_output(image, None, order=0)
-    data = resampled.get_fdata()
-
-    data = np.rot90(data, k=1, axes=(0, 1))
-
-    data[data < -1024] = -1024
-    data[data > 1024] = 1024
-
-    data = data - np.amin(data)
-    data = data / np.amax(data) * 255
-    data = data.astype("uint8")
-
-    print(data.shape)
-    return [data[..., i] for i in range(data.shape[-1])]
-
-
-def load_pred_volume_to_numpy(data_path):
-    if type(data_path) != str:
-        data_path = data_path.name
-
-    image = nib.load(data_path)
-    resampled = resample_to_output(image, None, order=0)
-    data = resampled.get_fdata()
-
-    data = np.rot90(data, k=1, axes=(0, 1))
-
-    data[data > 0] = 1
-    data = data.astype("uint8")
-
-    print(data.shape)
-    return [data[..., i] for i in range(data.shape[-1])]
-
-
-def nifti_to_glb(path, output="prediction.obj"):
-    # load NIFTI into numpy array
-    image = nib.load(path)
-    resampled = resample_to_output(image, [1, 1, 1], order=1)
-    data = resampled.get_fdata().astype("uint8")
-
-    # extract surface
-    verts, faces, normals, values = marching_cubes(data, 0)
-    faces += 1
-
-    with open(output, "w") as thefile:
-        for item in verts:
-            thefile.write("v {0} {1} {2}\n".format(item[0], item[1], item[2]))
-
-        for item in normals:
-            thefile.write("vn {0} {1} {2}\n".format(item[0], item[1], item[2]))
-
-        for item in faces:
-            thefile.write(
-                "f {0}//{0} {1}//{1} {2}//{2}\n".format(
-                    item[0], item[1], item[2]
-                )
-            )

app.py

@@ -1,41 +0,0 @@
-import os
-from argparse import ArgumentParser
-
-from AeroPath.gui import WebUI
-
-
-def main():
-    parser = ArgumentParser()
-    parser.add_argument(
-        "--cwd",
-        type=str,
-        default="/home/user/app/",
-        help="Set current working directory (path to app.py).",
-    )
-    parser.add_argument(
-        "--share",
-        type=int,
-        default=1,
-        help="Whether to enable the app to be accessible online"
-        "-> setups a public link which requires internet access.",
-    )
-    args = parser.parse_args()
-
-    print("Current working directory:", args.cwd)
-
-    if not os.path.exists(args.cwd):
-        raise ValueError("Chosen 'cwd' is not a valid path!")
-    if args.share not in [0, 1]:
-        raise ValueError(
-            "The 'share' argument can only be set to 0 or 1, but was:",
-            args.share,
-        )
-
-    # initialize and run app
-    print("Launching demo...")
-    app = WebUI(cwd=args.cwd, share=args.share)
-    app.run()
-
-
-if __name__ == "__main__":
-    main()

setup.cfg

@@ -4,11 +4,11 @@ description-file = README.md
 [isort]
 force_single_line=True
 known_first_party=aeropath
-line_length=80
+line_length=160
 profile=black
 
 [flake8]
 # imported but unused in __init__.py, that's ok.
 per-file-ignores=*__init__.py:F401
 ignore=E203,W503,W605,F632,E266,E731,E712,E741
-max-line-length=80
+max-line-length=160

shell/format.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+isort --sl demo/src/ demo/app.py
+black --line-length 80 demo/src/ demo/app.py
+flake8 demo/src/ demo/app.py

shell/lint.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+isort --check --sl -c demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+  exit 1
+fi
+echo "no issues with isort"
+flake8 demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please fix the code style issue."
+  exit 1
+fi
+echo "no issues with flake8"
+black --check --line-length 80 demo/src/ demo/app.py
+if ! [ $? -eq 0 ]
+then
+  echo "Please run \"sh shell/format.sh\" to format the code."
+    exit 1
+fi
+echo "no issues with black"
+echo "linting success!"