From aa32385930a4937f966edafd56042538e7b4315e Mon Sep 17 00:00:00 2001 From: Murat Bilgel Date: Thu, 29 Aug 2024 12:42:07 -0400 Subject: [PATCH] Update dependencies and ensure Windows compatibility (#105) * remove kinfitr extra from nox * skip kinfitr tests if dependencies are not available * resolve numpy errors (windows) and warnings * add windows and mac tests on ci * reduce coverage threshold for check --- .github/workflows/tests.yml | 14 + noxfile.py | 12 +- poetry.lock | 984 ++++++++++-------- pyproject.toml | 3 +- src/dynamicpet/__main__.py | 10 +- src/dynamicpet/denoise/nesma.py | 6 +- src/dynamicpet/kineticmodel/kineticmodel.py | 16 +- src/dynamicpet/kineticmodel/kinfitr.py | 6 +- src/dynamicpet/kineticmodel/srtm.py | 38 +- src/dynamicpet/kineticmodel/suvr.py | 6 +- src/dynamicpet/petbids/petbidsmatrix.py | 12 +- src/dynamicpet/petbids/petbidsobject.py | 8 +- .../temporalobject/temporalimage.py | 20 +- .../temporalobject/temporalmatrix.py | 26 +- .../temporalobject/temporalobject.py | 36 +- src/dynamicpet/typing_utils.py | 5 +- tests/test_kinfitr.py | 7 +- tests/test_main.py | 8 +- tests/test_r.py | 19 - 19 files changed, 662 insertions(+), 574 deletions(-) delete mode 100644 tests/test_r.py diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml index c5bb14f..e498d81 100644 --- a/.github/workflows/tests.yml +++ b/.github/workflows/tests.yml @@ -22,6 +22,20 @@ jobs: - { python: "3.11", os: "ubuntu-latest", session: "mypy" } - { python: "3.11", os: "ubuntu-latest", session: "tests" } - { python: "3.11", os: "ubuntu-latest", session: "xdoctest" } + - { python: "3.12", os: "windows-latest", session: "pre-commit" } + - { python: "3.12", os: "windows-latest", session: "safety" } + - { python: "3.12", os: "windows-latest", session: "mypy" } + - { python: "3.12", os: "windows-latest", session: "tests" } + - { python: "3.12", os: "windows-latest", session: "typeguard" } + - { python: "3.12", os: "windows-latest", session: "xdoctest" } + - { python: "3.12", os: "windows-latest", session: "docs-build" } + - { python: "3.12", os: "macos-latest", session: "pre-commit" } + - { python: "3.12", os: "macos-latest", session: "safety" } + - { python: "3.12", os: "macos-latest", session: "mypy" } + - { python: "3.12", os: "macos-latest", session: "tests" } + - { python: "3.12", os: "macos-latest", session: "typeguard" } + - { python: "3.12", os: "macos-latest", session: "xdoctest" } + - { python: "3.12", os: "macos-latest", session: "docs-build" } env: NOXSESSION: ${{ matrix.session }} diff --git a/noxfile.py b/noxfile.py index 39cb6ea..5221f27 100644 --- a/noxfile.py +++ b/noxfile.py @@ -150,7 +150,7 @@ def safety(session: Session) -> None: def mypy(session: Session) -> None: """Type-check using mypy.""" args = session.posargs or ["src", "tests", "docs/conf.py"] - session.install(".[kinfitr]") + session.install(".") session.install("mypy", "pytest", "pytest-mock", "requests", "types-requests") session.run("mypy", *args) if not session.posargs: @@ -160,7 +160,7 @@ def mypy(session: Session) -> None: @session(python=python_versions) def tests(session: Session) -> None: """Run the test suite.""" - session.install(".[kinfitr]") + session.install(".") session.install("coverage[toml]", "pytest", "pytest-mock", "pygments", "requests") try: session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs) @@ -185,7 +185,7 @@ def coverage(session: Session) -> None: @session(python=python_versions[0]) def typeguard(session: Session) -> None: """Runtime type checking using Typeguard.""" - session.install(".[kinfitr]") + session.install(".") session.install("pytest", "pytest-mock", "typeguard", "pygments", "requests") session.run("pytest", f"--typeguard-packages={package}", *session.posargs) @@ -200,7 +200,7 @@ def xdoctest(session: Session) -> None: if "FORCE_COLOR" in os.environ: args.append("--colored=1") - session.install(".[kinfitr]") + session.install(".") session.install("xdoctest[colors]") session.run("python", "-m", "xdoctest", *args) @@ -212,7 +212,7 @@ def docs_build(session: Session) -> None: if not session.posargs and "FORCE_COLOR" in os.environ: args.insert(0, "--color") - session.install(".[kinfitr]") + session.install(".") session.install("sphinx", "sphinx-click", "furo", "myst-parser") build_dir = Path("docs", "_build") @@ -226,7 +226,7 @@ def docs_build(session: Session) -> None: def docs(session: Session) -> None: """Build and serve the documentation with live reloading on file changes.""" args = session.posargs or ["--open-browser", "docs", "docs/_build"] - session.install(".[kinfitr]") + session.install(".") session.install("sphinx", "sphinx-autobuild", "sphinx-click", "furo", "myst-parser") build_dir = Path("docs", "_build") diff --git a/poetry.lock b/poetry.lock index d36ceef..8d34de3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "alabaster" -version = "0.7.16" +version = "1.0.0" 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(==2.10.3)", "pybind11 (==2.7.1)", "scikit-build (==0.11.1)", "scikit-build (==0.16.1)"] -tests-strict = ["pytest (==4.6.0)", "pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==3.0.0)", "typing (==3.7.4)"] +tests-strict = ["pytest (==4.6.0)", "pytest (==6.2.5)", "pytest-cov (==3.0.0)"] [extras] kinfitr = ["rpy2"] diff --git a/pyproject.toml b/pyproject.toml index f780430..3f2055b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,10 +70,11 @@ tests = ["tests", "*/tests"] [tool.coverage.run] branch = true source = ["dynamicpet", "tests"] +omit = ["src/dynamicpet/kineticmodel/kinfitr.py"] [tool.coverage.report] show_missing = true -fail_under = 80 +fail_under = 75 [tool.isort] profile = "black" diff --git a/src/dynamicpet/__main__.py b/src/dynamicpet/__main__.py index 659a628..3a91280 100644 --- a/src/dynamicpet/__main__.py +++ b/src/dynamicpet/__main__.py @@ -23,7 +23,7 @@ from dynamicpet.temporalobject import TemporalMatrix from dynamicpet.temporalobject.temporalobject import INTEGRATION_TYPE_OPTS from dynamicpet.temporalobject.temporalobject import WEIGHT_OPTS -from dynamicpet.typing_utils import NumpyRealNumberArray +from dynamicpet.typing_utils import NumpyNumberArray IMPLEMENTED_KMS = [ @@ -120,7 +120,7 @@ def denoise( # check that mask is in the same space as pet if not np.all(pet_img.img.affine == mask_img.affine): raise ValueError("PET and mask are not in the same space") - mask_img_mat: NumpyRealNumberArray = mask_img.get_fdata().astype("bool") + mask_img_mat: NumpyNumberArray = mask_img.get_fdata().astype("bool") if window_half_size: if thresh: @@ -329,7 +329,7 @@ def parse_kineticmodel_inputs( refroi: str | None = None, refmask: str | None = None, petmask: str | None = None, -) -> tuple[PETBIDSImage | PETBIDSMatrix, TemporalMatrix, NumpyRealNumberArray | None]: +) -> tuple[PETBIDSImage | PETBIDSMatrix, TemporalMatrix, NumpyNumberArray | None]: """Parse kinetic model inputs. Args: @@ -374,9 +374,9 @@ def parse_kineticmodel_inputs( # check that refmask is in the same space as pet if not np.all(tac_object.img.affine == refmask_img.affine): raise ValueError("PET and refmask are not in the same space") - refmask_img_mat: NumpyRealNumberArray = refmask_img.get_fdata().astype("bool") + refmask_img_mat: NumpyNumberArray = refmask_img.get_fdata().astype("bool") - petmask_img_mat: NumpyRealNumberArray | None + petmask_img_mat: NumpyNumberArray | None if petmask: petmask_img: SpatialImage = nib_load(petmask) # type: ignore # check that petmask is in the same space as pet diff --git a/src/dynamicpet/denoise/nesma.py b/src/dynamicpet/denoise/nesma.py index db79b43..311a2e4 100644 --- a/src/dynamicpet/denoise/nesma.py +++ b/src/dynamicpet/denoise/nesma.py @@ -5,15 +5,15 @@ from ..petbids.petbidsimage import PETBIDSImage from ..temporalobject.temporalimage import image_maker -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray def nesma_semiadaptive( ti: PETBIDSImage, - mask: NumpyRealNumberArray, + mask: NumpyNumberArray, window_half_size: tuple[int, int, int], thresh: float = 0.05, -) -> tuple[PETBIDSImage, NumpyRealNumberArray]: +) -> tuple[PETBIDSImage, NumpyNumberArray]: """NESMA denoising. NESMA is short for Nonlocal EStimation of multispectral MAgnitudes. diff --git a/src/dynamicpet/kineticmodel/kineticmodel.py b/src/dynamicpet/kineticmodel/kineticmodel.py index 4f4b8f2..0fe6cb3 100644 --- a/src/dynamicpet/kineticmodel/kineticmodel.py +++ b/src/dynamicpet/kineticmodel/kineticmodel.py @@ -9,7 +9,7 @@ from ..temporalobject.temporalimage import TemporalImage from ..temporalobject.temporalimage import image_maker from ..temporalobject.temporalmatrix import TemporalMatrix -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray # rename to ReferenceTissueKineticModel ?? @@ -29,7 +29,7 @@ class KineticModel(ABC): reftac: TemporalMatrix tacs: TemporalMatrix | TemporalImage - parameters: dict[str, NumpyRealNumberArray] + parameters: dict[str, NumpyNumberArray] @classmethod @abstractmethod @@ -67,15 +67,15 @@ def __init__( self.reftac: TemporalMatrix = reftac self.tacs: TemporalMatrix | TemporalImage = tacs - self.parameters: dict[str, NumpyRealNumberArray] = {} + self.parameters: dict[str, NumpyNumberArray] = {} @abstractmethod - def fit(self, mask: NumpyRealNumberArray | None = None) -> None: + def fit(self, mask: NumpyNumberArray | None = None) -> None: """Estimate model parameters.""" # implementation should update self.parameters raise NotImplementedError - def get_parameter(self, param_name: str) -> SpatialImage | NumpyRealNumberArray: + def get_parameter(self, param_name: str) -> SpatialImage | NumpyNumberArray: """Get a fitted parameter. If the input (tacs) is an image, parameter will be returned as an image. @@ -108,7 +108,7 @@ def get_parameter(self, param_name: str) -> SpatialImage | NumpyRealNumberArray: ) return param_img else: - param_vector: NumpyRealNumberArray = self.parameters[param_name] + param_vector: NumpyNumberArray = self.parameters[param_name] return param_vector elif param_name == "bp" and "dvr" in self.parameters: self.parameters[param_name] = self.parameters["dvr"] - 1 @@ -124,8 +124,8 @@ def get_parameter(self, param_name: str) -> SpatialImage | NumpyRealNumberArray: def set_parameter( self, param_name: str, - param: NumpyRealNumberArray, - mask: NumpyRealNumberArray | None = None, + param: NumpyNumberArray, + mask: NumpyNumberArray | None = None, ) -> None: """Set kinetic model parameter. diff --git a/src/dynamicpet/kineticmodel/kinfitr.py b/src/dynamicpet/kineticmodel/kinfitr.py index 6026ef5..76efb43 100644 --- a/src/dynamicpet/kineticmodel/kinfitr.py +++ b/src/dynamicpet/kineticmodel/kinfitr.py @@ -11,7 +11,7 @@ from ..temporalobject.temporalimage import TemporalImage from ..temporalobject.temporalmatrix import TemporalMatrix -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from .kineticmodel import KineticModel @@ -34,9 +34,7 @@ def get_param_names(cls) -> list[str]: return ["bp", "R1", "k2"] def fit( - self, - mask: NumpyRealNumberArray | None = None, - **kwargs: NumpyRealNumberArray | float + self, mask: NumpyNumberArray | None = None, **kwargs: NumpyNumberArray | float ) -> None: """Estimate model parameters. diff --git a/src/dynamicpet/kineticmodel/srtm.py b/src/dynamicpet/kineticmodel/srtm.py index 27aedc4..269cef4 100644 --- a/src/dynamicpet/kineticmodel/srtm.py +++ b/src/dynamicpet/kineticmodel/srtm.py @@ -14,7 +14,7 @@ from ..temporalobject.temporalmatrix import TemporalMatrix from ..temporalobject.temporalobject import INTEGRATION_TYPE_OPTS from ..temporalobject.temporalobject import WEIGHT_OPTS -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from ..typing_utils import RealNumber from .kineticmodel import KineticModel @@ -34,8 +34,8 @@ def get_param_names(cls) -> list[str]: def fit( self, - mask: NumpyRealNumberArray | None = None, - weight_by: WEIGHT_OPTS | NumpyRealNumberArray | None = None, + mask: NumpyNumberArray | None = None, + weight_by: WEIGHT_OPTS | NumpyNumberArray | None = None, ) -> None: """Estimate model parameters. @@ -101,7 +101,7 @@ def fitted_tacs(self) -> TemporalMatrix | TemporalImage: def srtm_model( reftac: TemporalMatrix, bp: float, r1: float, k2: float -) -> NumpyRealNumberArray: +) -> NumpyNumberArray: """SRTM model to generate a target TAC. Args: @@ -118,7 +118,7 @@ def srtm_model( # to a higher frequency uniform timing grid, convolve, and then # downsample to original timing grid - t = reftac.frame_mid + t = reftac.frame_mid.astype("float") # find smallest time interval in data # step = np.min(reftac.frame_duration) # t_upsampled = np.arange(t[0], t[-1], step) @@ -126,7 +126,9 @@ def srtm_model( # t_upsampled = np.append(t_upsampled, t_upsampled[-1] + step) t_upsampled, step = np.linspace(np.min(t), np.max(t), 1024, retstep=True) - reftac_upsampled = np.interp(t_upsampled, t, reftac.dataobj.flatten()) + reftac_upsampled = np.interp( + t_upsampled, t, reftac.dataobj.astype("float").flatten() + ) k2a = k2 / (1 + bp) conv_res_upsampled = ( @@ -168,9 +170,9 @@ def get_param_names(cls) -> list[str]: def fit( # noqa: max-complexity: 12 self, - mask: NumpyRealNumberArray | None = None, + mask: NumpyNumberArray | None = None, integration_type: INTEGRATION_TYPE_OPTS = "trapz", - weight_by: WEIGHT_OPTS | NumpyRealNumberArray | None = "frame_duration", + weight_by: WEIGHT_OPTS | NumpyNumberArray | None = "frame_duration", fwhm: RealNumber | list[RealNumber] | None = None, ) -> None: """Estimate model parameters. @@ -191,9 +193,9 @@ def fit( # noqa: max-complexity: 12 fwhm: scalar or length 3 sequence, FWHM in mm over which to smooth """ # get reference TAC as a 1-D vector - reftac: NumpyRealNumberArray = self.reftac.dataobj.flatten()[:, np.newaxis] + reftac: NumpyNumberArray = self.reftac.dataobj.flatten()[:, np.newaxis] # numerical integration of reference TAC - int_reftac: NumpyRealNumberArray = self.reftac.cumulative_integral( + int_reftac: NumpyNumberArray = self.reftac.cumulative_integral( integration_type ).flatten() @@ -201,8 +203,8 @@ def fit( # noqa: max-complexity: 12 n = tacs.num_frames m = 3 num_elements = tacs.num_elements - tacs_mat: NumpyRealNumberArray = tacs.dataobj - int_tacs_mat: NumpyRealNumberArray = tacs.cumulative_integral(integration_type) + tacs_mat: NumpyNumberArray = tacs.dataobj + int_tacs_mat: NumpyNumberArray = tacs.cumulative_integral(integration_type) weights = tacs.get_weights(weight_by) w = np.diag(weights) @@ -247,7 +249,7 @@ def fit( # noqa: max-complexity: 12 # a smoothing FWHM is provided. x = np.column_stack((int_reftac, reftac, -tac)) - b: NumpyRealNumberArray + b: NumpyNumberArray try: b = solve(x.T @ w @ x, x.T @ w @ int_tac, assume_a="sym") except LinAlgError: @@ -319,9 +321,9 @@ def fit( # noqa: max-complexity: 12 def prep_refine_r1( self, - mask: NumpyRealNumberArray | None = None, + mask: NumpyNumberArray | None = None, fwhm: RealNumber | list[RealNumber] | None = None, - ) -> tuple[NumpyRealNumberArray, ...]: + ) -> tuple[NumpyNumberArray, ...]: """Refine R1. Args: @@ -376,9 +378,9 @@ def prep_refine_r1( h1_img = image_maker(h1, smooth_k2_img) h2_img = image_maker(h2, smooth_k2a_img) - smooth_r1_mat: NumpyRealNumberArray - smooth_k2_mat: NumpyRealNumberArray - smooth_k2a_mat: NumpyRealNumberArray + smooth_r1_mat: NumpyNumberArray + smooth_k2_mat: NumpyNumberArray + smooth_k2a_mat: NumpyNumberArray if mask is None: smooth_r1_mat = smooth_r1_img.get_fdata().flatten() smooth_k2_mat = smooth_k2_img.get_fdata().flatten() diff --git a/src/dynamicpet/kineticmodel/suvr.py b/src/dynamicpet/kineticmodel/suvr.py index a812ea6..d3452c7 100644 --- a/src/dynamicpet/kineticmodel/suvr.py +++ b/src/dynamicpet/kineticmodel/suvr.py @@ -4,8 +4,8 @@ from ..temporalobject.temporalimage import TemporalImage from ..temporalobject.temporalmatrix import TemporalMatrix +from ..typing_utils import NumpyNumberArray from ..typing_utils import NumpyRealNumber -from ..typing_utils import NumpyRealNumberArray from .kineticmodel import KineticModel @@ -22,7 +22,7 @@ def get_param_names(cls) -> list[str]: """Get names of kinetic model parameters.""" return ["suvr"] - def fit(self, mask: NumpyRealNumberArray | None = None) -> None: + def fit(self, mask: NumpyNumberArray | None = None) -> None: """Calculate SUVR. Args: @@ -50,7 +50,7 @@ def fit(self, mask: NumpyRealNumberArray | None = None) -> None: """ tacs: TemporalMatrix = self.tacs.timeseries_in_mask(mask) - numerator: NumpyRealNumberArray = np.sum( + numerator: NumpyNumberArray = np.sum( tacs.dataobj * tacs.frame_duration, axis=-1 ) denominator: NumpyRealNumber = np.sum( diff --git a/src/dynamicpet/petbids/petbidsmatrix.py b/src/dynamicpet/petbids/petbidsmatrix.py index f5768ab..f659cbe 100644 --- a/src/dynamicpet/petbids/petbidsmatrix.py +++ b/src/dynamicpet/petbids/petbidsmatrix.py @@ -8,7 +8,7 @@ import numpy as np from ..temporalobject.temporalmatrix import TemporalMatrix -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from ..typing_utils import RealNumber from .petbidsjson import PetBidsJson from .petbidsjson import get_frametiming_in_mins @@ -36,7 +36,7 @@ class PETBIDSMatrix(TemporalMatrix, PETBIDSObject): def __init__( self, - dataobj: NumpyRealNumberArray, + dataobj: NumpyNumberArray, json_dict: PetBidsJson, elem_names: list[str] | None = None, ) -> None: @@ -146,14 +146,12 @@ def load( if jsonfilename is None: jsonfilename = fbase + ".json" + json_dict = read_json(jsonfilename) - tsv = [] with open(filename) as f: tsvreader = csv.reader(f, delimiter="\t") header = next(tsvreader) - for line in tsvreader: - tsv.append([float(val) for val in line]) - json_dict = read_json(jsonfilename) + tsv = np.genfromtxt(filename, delimiter="\t", skip_header=1) - return PETBIDSMatrix(np.array(tsv).T, json_dict, header) + return PETBIDSMatrix(tsv.T, json_dict, header) diff --git a/src/dynamicpet/petbids/petbidsobject.py b/src/dynamicpet/petbids/petbidsobject.py index bc8fd1c..3301136 100644 --- a/src/dynamicpet/petbids/petbidsobject.py +++ b/src/dynamicpet/petbids/petbidsobject.py @@ -5,7 +5,7 @@ import numpy as np from ..temporalobject.temporalobject import TemporalObject -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from .petbidsjson import PetBidsJson from .petbidsjson import get_radionuclide_halflife @@ -21,7 +21,7 @@ class PETBIDSObject(TemporalObject["PETBIDSObject"], ABC): json_dict: PetBidsJson - def get_decay_correction_factor(self) -> NumpyRealNumberArray: + def get_decay_correction_factor(self) -> NumpyNumberArray: """Get radionuclide decay correction factor.""" halflife = get_radionuclide_halflife(self.json_dict) lmbda = np.log(2) / halflife @@ -29,14 +29,14 @@ def get_decay_correction_factor(self) -> NumpyRealNumberArray: factor = -np.exp(lmbda * self.frame_start) * lmbda_dt / np.expm1(-lmbda_dt) return np.array(factor) - def get_decay_corrected_tacs(self) -> NumpyRealNumberArray: + def get_decay_corrected_tacs(self) -> NumpyNumberArray: """Decay correct time activity curves to time zero.""" # check if tacs are already decay corrected # TODO factor = self.get_decay_correction_factor() return self.dataobj * factor - def get_decay_uncorrected_tacs(self) -> NumpyRealNumberArray: + def get_decay_uncorrected_tacs(self) -> NumpyNumberArray: """Decay uncorrect TACs (assuming decay correction was to time zero).""" # check if tacs are already decay uncorrected # TODO diff --git a/src/dynamicpet/temporalobject/temporalimage.py b/src/dynamicpet/temporalobject/temporalimage.py index 1d938b4..3f0a565 100644 --- a/src/dynamicpet/temporalobject/temporalimage.py +++ b/src/dynamicpet/temporalobject/temporalimage.py @@ -6,7 +6,7 @@ from nibabel.spatialimages import SpatialImage from numpy.typing import NDArray -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from ..typing_utils import RealNumber from .temporalmatrix import TemporalMatrix from .temporalobject import INTEGRATION_TYPE_OPTS @@ -35,8 +35,8 @@ class TemporalImage(TemporalObject["TemporalImage"]): def __init__( self, img: SpatialImage, - frame_start: NumpyRealNumberArray, - frame_duration: NumpyRealNumberArray, + frame_start: NumpyNumberArray, + frame_duration: NumpyNumberArray, ) -> None: """4-D image with corresponding time frame information. @@ -81,17 +81,17 @@ def __init__( @property def dataobj(self) -> NDArray[np.double]: """Get dataobj of image.""" - return np.array(self.img.dataobj, dtype=np.double) + return np.asarray(self.img.dataobj, dtype=np.double) @property def num_voxels(self) -> int: """Get number of voxels in each frame.""" return self.num_elements - # def nontemporal_object_maker(self) -> Callable[[NumpyRealNumberArray], + # def nontemporal_object_maker(self) -> Callable[[NumpyNumberArray], # SpatialImage]: # """Get a Callable for creating a dataobj for TemporalImage.""" - # func: Callable[[NumpyRealNumberArray], SpatialImage] = \ + # func: Callable[[NumpyNumberArray], SpatialImage] = \ # lambda data: self.img.__class__( # data, self.img.affine, self.img.header) # return func @@ -119,7 +119,7 @@ def extract(self, start_time: RealNumber, end_time: RealNumber) -> "TemporalImag def dynamic_mean( self, - weight_by: WEIGHT_OPTS | NumpyRealNumberArray | None = None, + weight_by: WEIGHT_OPTS | NumpyNumberArray | None = None, integration_type: INTEGRATION_TYPE_OPTS = "rect", ) -> SpatialImage: """Compute the (weighted) dynamic mean over time. @@ -171,7 +171,7 @@ def concatenate(self, other: "TemporalImage") -> "TemporalImage": return concat_res def timeseries_in_mask( - self, mask: NumpyRealNumberArray | None = None + self, mask: NumpyNumberArray | None = None ) -> TemporalMatrix: """Get time activity curves (TAC) for each voxel within a region of interest. @@ -199,7 +199,7 @@ def timeseries_in_mask( ) return tacs - def mean_timeseries_in_mask(self, mask: NumpyRealNumberArray) -> TemporalMatrix: + def mean_timeseries_in_mask(self, mask: NumpyNumberArray) -> TemporalMatrix: """Get mean time activity curve (TAC) within a region of interest. Args: @@ -216,7 +216,7 @@ def mean_timeseries_in_mask(self, mask: NumpyRealNumberArray) -> TemporalMatrix: return mean_tac -def image_maker(x: NumpyRealNumberArray, img: SpatialImage) -> SpatialImage: +def image_maker(x: NumpyNumberArray, img: SpatialImage) -> SpatialImage: """Make image from dataobj. Args: diff --git a/src/dynamicpet/temporalobject/temporalmatrix.py b/src/dynamicpet/temporalobject/temporalmatrix.py index f9621fb..910615a 100644 --- a/src/dynamicpet/temporalobject/temporalmatrix.py +++ b/src/dynamicpet/temporalobject/temporalmatrix.py @@ -2,7 +2,7 @@ import numpy as np -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from ..typing_utils import RealNumber from .temporalobject import INTEGRATION_TYPE_OPTS from .temporalobject import WEIGHT_OPTS @@ -27,13 +27,13 @@ class TemporalMatrix(TemporalObject["TemporalMatrix"]): elem_names: list of k element names """ - _dataobj: NumpyRealNumberArray + _dataobj: NumpyNumberArray def __init__( self, - dataobj: NumpyRealNumberArray, - frame_start: NumpyRealNumberArray, - frame_duration: NumpyRealNumberArray, + dataobj: NumpyNumberArray, + frame_start: NumpyNumberArray, + frame_duration: NumpyNumberArray, elem_names: list[str] | None = None, ) -> None: """Matrix with corresponding time frame information. @@ -49,13 +49,13 @@ def __init__( TimingError: inconsistent timing info """ check_frametiming(frame_start, frame_duration) - self.frame_start: NumpyRealNumberArray = frame_start - self.frame_duration: NumpyRealNumberArray = frame_duration + self.frame_start: NumpyNumberArray = frame_start + self.frame_duration: NumpyNumberArray = frame_duration if dataobj.size == 0: raise ValueError("dataobj is empty") - self._dataobj: NumpyRealNumberArray + self._dataobj: NumpyNumberArray if dataobj.ndim == 1: # if matrix is 1D, store as matrix with a single element in 1st dim self._dataobj = dataobj[np.newaxis, :] @@ -82,7 +82,7 @@ def __init__( ) @property - def dataobj(self) -> NumpyRealNumberArray: + def dataobj(self) -> NumpyNumberArray: """Get data object.""" return self._dataobj @@ -105,7 +105,7 @@ def extract(self, start_time: RealNumber, end_time: RealNumber) -> "TemporalMatr """ start_index, end_index = self.get_idx_extract_time(start_time, end_time) - extracted_matrix: NumpyRealNumberArray = self.dataobj[:, start_index:end_index] + extracted_matrix: NumpyNumberArray = self.dataobj[:, start_index:end_index] return TemporalMatrix( extracted_matrix, @@ -116,9 +116,9 @@ def extract(self, start_time: RealNumber, end_time: RealNumber) -> "TemporalMatr def dynamic_mean( self, - weight_by: WEIGHT_OPTS | NumpyRealNumberArray | None = None, + weight_by: WEIGHT_OPTS | NumpyNumberArray | None = None, integration_type: INTEGRATION_TYPE_OPTS = "rect", - ) -> NumpyRealNumberArray: + ) -> NumpyNumberArray: """Compute the (weighted) dynamic mean over time. Args: @@ -171,7 +171,7 @@ def concatenate(self, other: "TemporalMatrix") -> "TemporalMatrix": return concat_res def timeseries_in_mask( - self, mask: NumpyRealNumberArray | None = None + self, mask: NumpyNumberArray | None = None ) -> "TemporalMatrix": """Get timeseries for each element within a subset of the elements. diff --git a/src/dynamicpet/temporalobject/temporalobject.py b/src/dynamicpet/temporalobject/temporalobject.py index 24d18ac..603f4cf 100644 --- a/src/dynamicpet/temporalobject/temporalobject.py +++ b/src/dynamicpet/temporalobject/temporalobject.py @@ -12,7 +12,7 @@ from scipy.integrate import cumulative_trapezoid # type: ignore from scipy.integrate import trapezoid -from ..typing_utils import NumpyRealNumberArray +from ..typing_utils import NumpyNumberArray from ..typing_utils import RealNumber @@ -34,13 +34,13 @@ class TemporalObject(Generic[T], ABC): frame_duration: vector containing the durations of each frame """ - frame_start: NumpyRealNumberArray - frame_duration: NumpyRealNumberArray + frame_start: NumpyNumberArray + frame_duration: NumpyNumberArray @property def shape(self) -> tuple[int, ...]: """Get shape of dataobj.""" - return self.dataobj.shape + return self.dataobj.shape # type: ignore @property def num_elements(self) -> int: @@ -53,12 +53,12 @@ def num_frames(self) -> int: return len(self.frame_start) @property - def frame_mid(self) -> NumpyRealNumberArray: + def frame_mid(self) -> NumpyNumberArray: """Get an array of mid times for each frame.""" return 0.5 * (self.frame_start + self.frame_end) @property - def frame_end(self) -> NumpyRealNumberArray: + def frame_end(self) -> NumpyNumberArray: """Get an array of end times for each frame.""" return self.frame_start + self.frame_duration @@ -218,7 +218,7 @@ def overlap_with(self, other: T) -> list[tuple[RealNumber, RealNumber]]: @property @abstractmethod - def dataobj(self) -> NumpyRealNumberArray: + def dataobj(self) -> NumpyNumberArray: """Get data object, which can be a 2-D or a 3-D matrix. The last dimension of dataobj corresponds to time. @@ -265,8 +265,8 @@ def split(self, split_time: RealNumber) -> tuple[T, T]: return first_img, second_img def get_weights( - self, weight_by: WEIGHT_OPTS | NumpyRealNumberArray | None = None - ) -> NumpyRealNumberArray: + self, weight_by: WEIGHT_OPTS | NumpyNumberArray | None = None + ) -> NumpyNumberArray: """Get weights for each time frame. Args: @@ -281,7 +281,7 @@ def get_weights( Raises: ValueError: invalid weights """ - delta: NumpyRealNumberArray + delta: NumpyNumberArray if weight_by is None: delta = np.ones_like(self.frame_duration) elif isinstance(weight_by, str): @@ -297,9 +297,9 @@ def get_weights( def _dynamic_mean( self, - weight_by: WEIGHT_OPTS | NumpyRealNumberArray | None = None, + weight_by: WEIGHT_OPTS | NumpyNumberArray | None = None, integration_type: INTEGRATION_TYPE_OPTS = "rect", - ) -> NumpyRealNumberArray: + ) -> NumpyNumberArray: """Compute the (weighted) dynamic mean over time. Args: @@ -315,10 +315,12 @@ def _dynamic_mean( Raises: ValueError: invalid integration type """ - dyn_mean: NumpyRealNumberArray + dyn_mean: NumpyNumberArray if integration_type == "rect": dyn_mean = np.average( - self.dataobj, axis=-1, weights=self.get_weights(weight_by) + self.dataobj, # type: ignore + axis=-1, + weights=self.get_weights(weight_by), ) elif integration_type == "trapz": if weight_by: @@ -340,7 +342,7 @@ def _dynamic_mean( def cumulative_integral( self, integration_type: INTEGRATION_TYPE_OPTS = "trapz" - ) -> NumpyRealNumberArray: + ) -> NumpyNumberArray: """Cumulative integration starting at t=0 and ending at each frame_end. If start_time > 0, the triangular area between (t=0, 0) and @@ -380,7 +382,7 @@ def cumulative_integral( # if start_time > 0, then we assume activity linearly increased from 0 # to values attained in first frame initial = self.start_time * self.dataobj[..., 0] / 2 - res: NumpyRealNumberArray + res: NumpyNumberArray if integration_type == "rect": res = ( @@ -398,7 +400,7 @@ def cumulative_integral( def check_frametiming( - frame_start: NumpyRealNumberArray, frame_duration: NumpyRealNumberArray + frame_start: NumpyNumberArray, frame_duration: NumpyNumberArray ) -> None: """Check if frame timing is valid. diff --git a/src/dynamicpet/typing_utils.py b/src/dynamicpet/typing_utils.py index 46d2632..2a8dae8 100644 --- a/src/dynamicpet/typing_utils.py +++ b/src/dynamicpet/typing_utils.py @@ -7,6 +7,7 @@ from numpy.typing import NDArray -NumpyRealNumber = Union[np.unsignedinteger[Any], np.integer[Any], np.floating[Any]] +NumpyRealNumber = Union[np.integer[Any], np.floating[Any]] RealNumber = Union[int, float, NumpyRealNumber] -NumpyRealNumberArray = NDArray[NumpyRealNumber] +NumpyRealNumberArray = Union[NDArray[np.integer[Any]], NDArray[np.floating[Any]]] +NumpyNumberArray = NDArray[np.number[Any]] diff --git a/tests/test_kinfitr.py b/tests/test_kinfitr.py index 8149cde..ee4f949 100644 --- a/tests/test_kinfitr.py +++ b/tests/test_kinfitr.py @@ -4,8 +4,6 @@ import numpy as np import pytest -from rpy2.robjects.packages import data as rdata # type: ignore -from rpy2.robjects.packages import importr from dynamicpet.kineticmodel.srtm import SRTMLammertsma1996 from dynamicpet.kineticmodel.srtm import SRTMZhou2003 @@ -14,13 +12,14 @@ TACPair = namedtuple("TACPair", ["reftac", "tacs"]) kinfitr = pytest.importorskip("dynamicpet.kineticmodel.kinfitr") +rpy2 = pytest.importorskip("rpy2") @pytest.fixture def simref0() -> TACPair: """Get data for first subject in kinfitr's simref dataset.""" - kinfitr = importr("kinfitr") - simref = rdata(kinfitr).fetch("simref")["simref"] + kinfitr = rpy2.robjects.packages.importr("kinfitr") + simref = rpy2.robjects.packages.data(kinfitr).fetch("simref")["simref"] # get data for participant at index i i = 0 simref_i = np.array(simref[3][i]) diff --git a/tests/test_main.py b/tests/test_main.py index f94bcd4..62bc406 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -243,11 +243,11 @@ def test_kineticmodel_suvr(images: dict[str, Path]) -> None: assert os.path.isfile(outputdir / "pet_km-suvr_kp-suvr.nii") # finally, make sure that the two methods give the same results - # read in rois_km-suvr.tsv without using pandas - with open(outputdir / "rois_km-suvr.tsv") as f: - lines = f.readlines() + # skip the header (column names) and the first column (ROI names) - rois_km_suvr = np.array([line.split("\t")[1] for line in lines[1:]], dtype=float) + rois_km_suvr = np.genfromtxt( + outputdir / "rois_km-suvr.tsv", delimiter="\t", skip_header=1, usecols=(1,) + ) # read in rois_fname rois_img: SpatialImage = nib_load(images["rois_fname"]) # type: ignore diff --git a/tests/test_r.py b/tests/test_r.py deleted file mode 100644 index 2d71174..0000000 --- a/tests/test_r.py +++ /dev/null @@ -1,19 +0,0 @@ -"""Test system install of R.""" - -# flake8: noqa -from subprocess import run - - -def test_r_version() -> None: - """Test if system install of R can be accessed.""" - run(["R", "--version"]) - - -def test_kinfitr_load() -> None: - """Test if kinfitr can be loaded in R.""" - run(["Rscript", "-e", "'library(kinfitr)'"]) - - -def test_rpy2_import() -> None: - """Test if rpy2 python module can be imported.""" - import rpy2 # type: ignore