remove kinfitr

README.md

@@ -53,11 +53,6 @@ _Dynamic PET_ requires Python 3.11+ and the following modules:
 `nibabel` for neuroimaging data I/O and simple manipulations, and
 `click` for the CLI.
 
-To run the `kinfitr` implementations of kinetic models, you will also need an
-installation of R and the [kinfitr] R package as well as the `rpy2` Python module.
-
-[kinfitr]: https://github.com/mathesong/kinfitr
-
 ## Installation
 
 You can install _Dynamic PET_ via [pip] after cloning the repository:
@@ -67,18 +62,6 @@ $ git clone https://github.com/bilgelm/dynamicpet.git
 $ pip install -e dynamicpet
 ```
 
-If you would like to use kinetic models implemented in `kinfitr` with
-_Dynamic PET_, first [install R](https://cran.r-project.org)
-and the [kinfitr] R package.
-Then install _Dynamic PET_ with the `kinfitr` extra after cloning the `git`
-repository as descibed above:
-
-```console
-$ pip install -e dynamicpet[kinfitr]
-```
-
-[kinfitr]: https://github.com/mathesong/kinfitr
-
 ## Usage
 
 Please see the [Usage] for details on the CLI.

docs/api.md

@@ -47,7 +47,8 @@
 
 ## dynamicpet.kineticmodel
 
-These kinetic model implementations use the entire temporal extent of the TAC object provided for modeling. If you'd like to use a specific time interval for
+These kinetic model implementations use the entire temporal extent of the TAC
+object provided for modeling. If you'd like to use a specific time interval for
 modeling, first extract this time interval and then fit the kinetic model.
 
 ```{eval-rst}
@@ -61,9 +62,3 @@ modeling, first extract this time interval and then fit the kinetic model.
    :members:
    :inherited-members:
 ```
-
-```{eval-rst}
-.. automodule:: dynamicpet.kineticmodel.kinfitr
-   :members:
-   :inherited-members:
-```

pyproject.toml

@@ -22,13 +22,8 @@ numpy = ">=1.24.3"
 click = ">=8.1.3"
 scipy = ">=1.10.1"
 tqdm = ">=4.65.0"
-
-rpy2 = { version = ">=3.5.12", optional = true }
 types-tqdm = "^4.66.0.20240417"
 
-[tool.poetry.extras]
-kinfitr = ["rpy2"]
-
 [tool.poetry.scripts]
 kineticmodel = "dynamicpet.__main__:kineticmodel"
 denoise = "dynamicpet.__main__:denoise"

src/dynamicpet/__main__.py

@@ -30,8 +30,6 @@
     "SUVR",
     "SRTMLammertsma1996",
     "SRTMZhou2003",
-    "kinfitr.SRTM",
-    "kinfitr.SRTM2",
 ]
 
 INTEGRATION_TYPES = (
@@ -281,16 +279,6 @@ def kineticmodel(
                 weight_by=weight_by,
                 fwhm=fwhm,
             )
-        case "kinfitr.srtm":
-            from dynamicpet.kineticmodel import kinfitr
-
-            km = kinfitr.SRTM(reftac, pet_img)
-            km.fit(mask=petmask_img_mat)
-        case "kinfitr.srtm2":
-            from dynamicpet.kineticmodel import kinfitr
-
-            km = kinfitr.SRTM2(reftac, pet_img)
-            km.fit(mask=petmask_img_mat)
         case _:
             raise ValueError(f"Model {model} is not supported")
 

tests/test_kineticmodel_simulated.py

@@ -268,30 +268,3 @@ def test_srtmlammertsma1996_tm(
     assert np.allclose(bp, bp_true, rtol=relative_tol)
     assert np.allclose(r1, r1_true, rtol=relative_tol)
     assert np.allclose(fitted_tacs.dataobj, tac.dataobj, rtol=relative_tol)
-
-
-def test_srtmkinfitr_tm(
-    frame_start: NDArray[np.double],
-    frame_duration: NDArray[np.double],
-) -> None:
-    """Test kinfitr SRTM wrapper."""
-    kinfitr = pytest.importorskip("dynamicpet.kineticmodel.kinfitr")
-
-    bp_true = 1.5
-    r1_true = 1.2
-    ct, cref = get_tacs_and_reftac_dataobj(
-        frame_start, frame_duration, bp_true, r1_true
-    )
-
-    tac = TemporalMatrix(ct, frame_start, frame_duration)
-    reftac = TemporalMatrix(cref, frame_start, frame_duration)
-
-    km = kinfitr.SRTM(reftac, tac)
-    km.fit()
-
-    bp: NumpyRealNumberArray = km.get_parameter("bp")
-    r1: NumpyRealNumberArray = km.get_parameter("R1")
-
-    relative_tol = 0.006
-    assert np.allclose(bp, bp_true, rtol=relative_tol)
-    assert np.allclose(r1, r1_true, rtol=relative_tol)