Merge pull request #83 from JoHof/fix/no_download_when_path

Fix/no download when path

lungmask/__main__.py

@@ -7,7 +7,7 @@
 import pkg_resources  # type: ignore
 import SimpleITK as sitk
 
-from lungmask import mask, utils
+from lungmask import LMInferer, utils
 
 
 def path(string):
@@ -48,7 +48,6 @@ def main():
     parser.add_argument(
         "--classes",
         help="spcifies the number of output classes of the model",
-        default=3,
     )
     parser.add_argument(
         "--cpu",
@@ -86,6 +85,11 @@ def main():
     argsin = sys.argv[1:]
     args = parser.parse_args(argsin)
 
+    if args.classes is not None:
+        logging.warn(
+            "!!! Warning: The `classes` parameter is deprecated and will be removed in the next version !!!"
+        )
+
     batchsize = args.batchsize
     if args.cpu:
         batchsize = 1
@@ -98,29 +102,30 @@ def main():
         assert (
             args.modelpath is None
         ), "Modelpath can not be specified for LTRCLobes_R231 mode"
-        result = mask.apply_fused(
-            input_image,
+        inferer = LMInferer(
+            modelname="LTRCLobes",
             force_cpu=args.cpu,
+            fillmodel="R231",
             batch_size=batchsize,
             volume_postprocessing=not (args.nopostprocess),
             noHU=args.noHU,
             tqdm_disable=args.noprogress,
         )
+        result = inferer.apply(input_image)
     else:
-        model = mask.get_model(args.modelname, args.modelpath, args.classes)
-        result = mask.apply(
-            input_image,
-            model,
+        inferer = LMInferer(
+            modelname=args.modelname,
+            modelpath=args.modelpath,
             force_cpu=args.cpu,
             batch_size=batchsize,
             volume_postprocessing=not (args.nopostprocess),
             noHU=args.noHU,
             tqdm_disable=args.noprogress,
         )
+        result = inferer.apply(input_image)
 
     if args.noHU:
         file_ending = args.output.split(".")[-1]
-        print(file_ending)
         if file_ending in ["jpg", "jpeg", "png"]:
             result = (result / (result.max()) * 255).astype(np.uint8)
         result = result[0]

lungmask/mask.py

@@ -1,4 +1,5 @@
 import logging
+import os
 import sys
 import warnings
 from typing import Optional, Union
@@ -41,15 +42,12 @@
 }
 
 
-def get_model(
-    modelname: str, modelpath: Optional[str] = None, n_classes: int = 3
-) -> torch.nn.Module:
+def get_model(modelname: str, modelpath: Optional[str] = None) -> torch.nn.Module:
     """Loads specific model and state
 
     Args:
         modelname (str): Modelname (e.g. R231, LTRCLobes or R231CovidWeb)
         modelpath (Optional[str], optional): Path to statedict, if not provided will be downloaded automatically. Modelname will be ignored if provided. Defaults to None.
-        n_classes (int, optional): Number of classes. Will be automatically set if modelname is provided. Defaults to 3.
 
     Returns:
         torch.nn.Module: Loaded model in eval state
@@ -62,6 +60,8 @@ def get_model(
     else:
         state_dict = torch.load(modelpath, map_location=torch.device("cpu"))
 
+    n_classes = len(list(state_dict.values())[-1])
+
     model = UNet(
         n_classes=n_classes,
         padding=True,
@@ -78,19 +78,23 @@ def get_model(
 class LMInferer:
     def __init__(
         self,
-        modelname="R231",
+        modelname: str = "R231",
+        modelpath: Optional[str] = None,
         fillmodel: Optional[str] = None,
-        force_cpu=False,
-        batch_size=20,
-        volume_postprocessing=True,
-        noHU=False,
-        tqdm_disable=False,
+        fillmodel_path: Optional[str] = None,
+        force_cpu: bool = False,
+        batch_size: int = 20,
+        volume_postprocessing: bool = True,
+        noHU: bool = False,
+        tqdm_disable: bool = False,
     ):
         """LungMaskInference
 
         Args:
             modelname (str, optional): Model to be applied. Defaults to 'R231'.
+            modelpath (str, optional): Path to modeleights. `modelname` parameter will be ignored if provided. Defaults to None.
             fillmodel (Optional[str], optional): Fillmodel to be applied. Defaults to None.
+            fillmodel_path (Optional[str], optional): Path to weights for fillmodel. `fillmodel` parameter will be ignored if provided. Defaults to None.
             force_cpu (bool, optional): Will not use GPU is `True`. Defaults to False.
             batch_size (int, optional): Batch size. Defaults to 20.
             volume_postprocessing (bool, optional): If `Fales` will not perform postprocessing (connected component analysis). Defaults to True.
@@ -104,6 +108,13 @@ def __init__(
             assert (
                 fillmodel in MODEL_URLS
             ), "Modelname not found. Please choose from: {}".format(MODEL_URLS.keys())
+
+        # if paths provided, overwrite name
+        if modelpath is not None:
+            modelname = os.path.basename(modelpath)
+        if fillmodel_path is not None:
+            fillmodel = os.path.basename(fillmodel_path)
+
         self.fillmodel = fillmodel
         self.modelname = modelname
         self.force_cpu = force_cpu
@@ -112,7 +123,7 @@ def __init__(
         self.noHU = noHU
         self.tqdm_disable = tqdm_disable
 
-        self.model = get_model(self.modelname)
+        self.model = get_model(self.modelname, modelpath)
 
         self.device = torch.device("cpu")
         if not self.force_cpu:
@@ -124,7 +135,7 @@ def __init__(
 
         self.fillmodelm = None
         if self.fillmodel is not None:
-            self.fillmodelm = get_model(self.fillmodel)
+            self.fillmodelm = get_model(self.fillmodel, fillmodel_path)
             self.fillmodelm.to(self.device)
 
     def _inference(
@@ -250,6 +261,10 @@ def apply(
     noHU=False,
     tqdm_disable=False,
 ):
+    warnings.warn(
+        "The function `apply` will be removed in a future version. Please use the LMInferer class!",
+        DeprecationWarning,
+    )
     inferer = LMInferer(
         force_cpu=force_cpu,
         batch_size=batch_size,
@@ -272,6 +287,10 @@ def apply_fused(
     noHU=False,
     tqdm_disable=False,
 ):
+    warnings.warn(
+        "The function `apply_fused` will be removed in a future version. Please use the LMInferer class!",
+        DeprecationWarning,
+    )
     inferer = LMInferer(
         modelname=basemodel,
         force_cpu=force_cpu,

lungmask/utils.py

@@ -252,6 +252,7 @@ def postprocessing(
     Returns:
         np.ndarray: Postprocessed volume
     """
+    logging.info("Postprocessing")
 
     # CC analysis
     regionmask = skimage.measure.label(label_image)

setup.py

@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="lungmask",
-    version="0.2.14",
+    version="0.2.15",
     author="Johannes Hofmanninger",
     author_email="[email protected]",
     description="Package for automated lung segmentation in CT",

tests/test_mask.py

@@ -1,10 +1,11 @@
 import os
+import shutil
 
 import numpy as np
-import pydicom as pyd
 import pytest
+import torch
 
-from lungmask.mask import LMInferer, apply, apply_fused
+from lungmask.mask import MODEL_URLS, LMInferer
 from lungmask.utils import read_dicoms
 
 
@@ -13,13 +14,47 @@ def fixture_testvol():
     return read_dicoms(os.path.join(os.path.dirname(__file__), "testdata"))[0]
 
 
-def test_apply(fixture_testvol):
-    res = apply(fixture_testvol)
+@pytest.fixture(scope="session")
+def fixture_weights_path_R231(tmpdir_factory):
+    # we make sure the model is there
+    torch.hub.load_state_dict_from_url(
+        MODEL_URLS["R231"][0], progress=True, map_location=torch.device("cpu")
+    )
+    modelbasename = os.path.basename(MODEL_URLS["R231"][0])
+    modelpath = os.path.join(torch.hub.get_dir(), "checkpoints", modelbasename)
+    tmppath = str(tmpdir_factory.mktemp("weights").join(modelbasename))
+    shutil.copy(modelpath, tmppath)
+    return tmppath
+
+
+def test_LMInferer(fixture_testvol, fixture_weights_path_R231):
+    inferer = LMInferer(
+        force_cpu=True,
+        tqdm_disable=True,
+    )
+    res = inferer.apply(fixture_testvol)
     assert np.all(np.unique(res, return_counts=True)[1] == [423000, 64752, 36536])
 
+    # here, we provide a path to the R231 weights but specify LTRCLobes (6 channel) as modelname
+    # The modelname should be ignored and a 3 channel output should be generated
+    inferer = LMInferer(
+        modelname="LTRCLobes",
+        modelpath=fixture_weights_path_R231,
+        force_cpu=True,
+        tqdm_disable=True,
+    )
+    res = inferer.apply(fixture_testvol)
+    assert np.all(np.unique(res, return_counts=True)[1] == [423000, 64752, 36536])
 
-def test_apply_fused(fixture_testvol):
-    res = apply_fused(fixture_testvol)
+
+def test_LMInferer_fused(fixture_testvol):
+    inferer = LMInferer(
+        modelname="LTRCLobes",
+        force_cpu=True,
+        fillmodel="R231",
+        tqdm_disable=True,
+    )
+    res = inferer.apply(fixture_testvol)
     assert np.all(
         np.unique(res, return_counts=True)[1] == [423000, 13334, 23202, 23834, 40918]
     )

tests/test_utils.py

@@ -1,10 +1,7 @@
 import os
 
 import numpy as np
-import pydicom as pd
-import pydicom as pyd
 import SimpleITK as sitk
-from pydicom.dataset import FileMetaDataset
 
 from lungmask.utils import (
     bbox_3D,
@@ -18,6 +15,9 @@
 )
 
 # creating test dicom data for reference
+# import pydicom as pd
+# import pydicom as pyd
+# from pydicom.dataset import FileMetaDataset
 #
 # studyuid = pyd.uid.generate_uid()
 # seriesuid = pyd.uid.generate_uid()