Merge pull request #3 from kaitj/enh/io_functions

Add IO functions

.github/pull_request_template.md

@@ -1,24 +1,18 @@
 **Proposed changes**
-Describe the changes implemented in this pull request. If the changes fix a 
-bug or resolves a feature request, be sure to link the issue. Please explain 
-the issue and how the changes address the issue.
+Describe the changes implemented in this pull request. If the changes fix a bug or resolves a feature request, be sure to link the issue. Please explain the issue and how the changes address the issue.
 
 **Types of changes**
-What types of changes does your code introduce? Put an `x` in the boxes that 
-apply
+What types of changes does your code introduce? Put an `x` in the boxes that apply
 
 - [ ] Bugfix (non-breaking change which fixes an issue)
 - [ ] New feature (non-breaking change which adds functionality)
-- [ ] Breaking change (fix or feature that would cause existing functionality 
-to not work as expected)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
 - [ ] Other (if none of the other choices apply)
 
 **Checklist**
-Put an `x` in the boxes that apply. You can also fill these out after creating 
-the PR. If you are unsure about any of the choices, don't hesitate to ask!
+Put an `x` in the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!
 
-- [ ] Changes have been tested to ensure that fix is effective or that a 
-feature works.
+- [ ] Changes have been tested to ensure that fix is effective or that a feature works.
 - [ ] Changes pass the unit tests
 - [ ] Code has been run through the `poe quality` task
 - [ ] I have included necessary documentation or comments (as necessary)

.github/workflows/test.yml

@@ -76,7 +76,13 @@ jobs:
             }}
       - name: Install dependencies
         if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root --with dev
-        # Example of test
-      # - name: Test minimum inputs
-        # run: poetry run poe test_base
+        run: poetry install --no-interaction --no-root --with dev 
+      - name: Install library
+        run: poetry install --no-interaction --with dev
+      - name: Perform unit testing
+        run: poetry run poe test_cov
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}        
+          files: ../cov.xml

.gitignore

@@ -0,0 +1,7 @@
+# Directories
+__pycache__/
+
+# Testing
+.hypothesis
+.ruff_cache
+.pytest_cache

afids_utils/__init__.py

@@ -0,0 +1 @@
+"""Top-level for afids-utils."""

afids_utils/exceptions.py

@@ -0,0 +1,8 @@
+"""Custom exceptions"""
+
+
+class InvalidFiducialNumberError(Exception):
+    """Exception for invalid fiducial number"""
+
+    def __init__(self, fid_num: int) -> None:
+        super().__init__(f"Provided fiducial {fid_num} is not valid.")

afids_utils/io.py

@@ -0,0 +1,70 @@
+"""Methods for loading and saving nifti files"""
+from __future__ import annotations
+
+import csv
+from importlib import resources
+from os import PathLike
+
+import numpy as np
+import pandas as pd
+from numpy.typing import NDArray
+
+from afids_utils.exceptions import InvalidFiducialNumberError
+
+FCSV_FIELDNAMES = [
+    "# columns = id",
+    "x",
+    "y",
+    "z",
+    "ow",
+    "ox",
+    "oy",
+    "oz",
+    "vis",
+    "sel",
+    "lock",
+    "label",
+    "desc",
+    "associatedNodeID",
+]
+
+
+def get_afid(
+    fcsv_path: PathLike[str] | str, fid_num: int
+) -> NDArray[np.single]:
+    """Extract specific fiducial's spatial coordinates"""
+    if fid_num < 1 or fid_num > 32:
+        raise InvalidFiducialNumberError(fid_num)
+    fcsv_df = pd.read_csv(
+        fcsv_path, sep=",", header=2, usecols=FCSV_FIELDNAMES
+    )
+
+    return fcsv_df.loc[fid_num - 1, ["x", "y", "z"]].to_numpy(dtype="single")
+
+
+def afids_to_fcsv(
+    afid_coords: NDArray[np.single],
+    fcsv_output: PathLike[str] | str,
+) -> None:
+    """AFIDS to Slicer-compatible .fcsv file"""
+    # Read in fcsv template
+    with resources.open_text(
+        "afids_utils.resources", "template.fcsv"
+    ) as template_fcsv_file:
+        header = [template_fcsv_file.readline() for _ in range(3)]
+        reader = csv.DictReader(template_fcsv_file, fieldnames=FCSV_FIELDNAMES)
+        fcsv = list(reader)
+
+    # Loop over fiducials and update with fiducial spatial coordinates
+    for idx, row in enumerate(fcsv):
+        row["x"] = afid_coords[idx][0]
+        row["y"] = afid_coords[idx][1]
+        row["z"] = afid_coords[idx][2]
+
+    # Write output fcsv
+    with open(fcsv_output, "w", encoding="utf-8", newline="") as out_fcsv_file:
+        for line in header:
+            out_fcsv_file.write(line)
+        writer = csv.DictWriter(out_fcsv_file, fieldnames=FCSV_FIELDNAMES)
+        for row in fcsv:
+            writer.writerow(row)

afids_utils/resources/template.fcsv

@@ -0,0 +1,35 @@
+# Markups fiducial file version = 4.6
+# CoordinateSystem = 0
+# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
+vtkMRMLMarkupsFiducialNode_1,0,0,0,0,0,0,1,1,1,1,1,AC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_2,0,0,0,0,0,0,1,1,1,1,2,PC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_3,0,0,0,0,0,0,1,1,1,1,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_4,0,0,0,0,0,0,1,1,1,1,4,PMJ,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_5,0,0,0,0,0,0,1,1,1,1,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_6,0,0,0,0,0,0,1,1,1,1,6,R superior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_7,0,0,0,0,0,0,1,1,1,1,7,L superior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_8,0,0,0,0,0,0,1,1,1,1,8,R inferior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_9,0,0,0,0,0,0,1,1,1,1,9,L inferior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_10,0,0,0,0,0,0,1,1,1,1,10,culmen,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_11,0,0,0,0,0,0,1,1,1,1,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_12,0,0,0,0,0,0,1,1,1,1,12,R MB,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_13,0,0,0,0,0,0,1,1,1,1,13,L MB,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_14,0,0,0,0,0,0,1,1,1,1,14,pineal gland,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_15,0,0,0,0,0,0,1,1,1,1,15,R LV at AC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_16,0,0,0,0,0,0,1,1,1,1,16,L LV at AC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_17,0,0,0,0,0,0,1,1,1,1,17,R LV at PC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_18,0,0,0,0,0,0,1,1,1,1,18,L LV at PC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_19,0,0,0,0,0,0,1,1,1,1,19,genu of CC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_20,0,0,0,0,0,0,1,1,1,1,20,splenium,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_21,0,0,0,0,0,0,1,1,1,1,21,R AL temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_22,0,0,0,0,0,0,1,1,1,1,22,L AL temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_23,0,0,0,0,0,0,1,1,1,1,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_24,0,0,0,0,0,0,1,1,1,1,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_25,0,0,0,0,0,0,1,1,1,1,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_26,0,0,0,0,0,0,1,1,1,1,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_27,0,0,0,0,0,0,1,1,1,1,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_28,0,0,0,0,0,0,1,1,1,1,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_29,0,0,0,0,0,0,1,1,1,1,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_30,0,0,0,0,0,0,1,1,1,1,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_31,0,0,0,0,0,0,1,1,1,1,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_32,0,0,0,0,0,0,1,1,1,1,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1

afids_utils/tests/data/tpl-MNI152NLin2009cAsym_afids.fcsv

@@ -0,0 +1,35 @@
+# Markups fiducial file version = 4.6
+# CoordinateSystem = 0
+# columns = id,x,y,z,ow,ox,oy,oz,vis,sel,lock,label,desc,associatedNodeID
+vtkMRMLMarkupsFiducialNode_1,-0.23099999999999998,2.93275,-4.899,0,0,0,1,1,1,0,1,AC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_2,-0.24125000000000002,-25.074749999999998,-2.169,0,0,0,1,1,1,0,2,PC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_3,0.19949999999999998,-37.268249999999995,-10.9115,0,0,0,1,1,1,0,3,infracollicular sulcus,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_4,-0.12725000000000003,-23.14825,-21.522,0,0,0,1,1,1,0,4,PMJ,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_5,-0.06675,-14.81275,-11.32025,0,0,0,1,1,1,0,5,superior interpeduncular fossa,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_6,12.67275,-26.960749999999997,-10.38225,0,0,0,1,1,1,0,6,R superior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_7,-13.004999999999999,-27.190749999999998,-10.32375,0,0,0,1,1,1,0,7,L superior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_8,10.873,-30.96475,-21.533,0,0,0,1,1,1,0,8,R inferior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_9,-11.18,-30.437000000000005,-21.537,0,0,0,1,1,1,0,9,L inferior LMS,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_10,-0.004750000000000004,-52.3695,2.06825,0,0,0,1,1,1,0,10,culmen,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_11,-0.0665,-8.131499999999999,-14.7755,0,0,0,1,1,1,0,11,intermammillary sulcus,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_12,2.0255,-8.143500000000001,-14.752749999999999,0,0,0,1,1,1,0,12,R MB,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_13,-2.3954999999999997,-8.0565,-14.8675,0,0,0,1,1,1,0,13,L MB,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_14,0.04425,-31.73675,0.76675,0,0,0,1,1,1,0,14,pineal gland,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_15,15.141750000000002,5.3445,24.358249999999998,0,0,0,1,1,1,0,15,R LV at AC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_16,-15.6095,5.22575,24.63125,0,0,0,1,1,1,0,16,L LV at AC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_17,18.4955,-22.061999999999998,27.66,0,0,0,1,1,1,0,17,R LV at PC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_18,-18.999000000000002,-22.046,27.284,0,0,0,1,1,1,0,18,L LV at PC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_19,0.17799999999999996,33.423500000000004,2.6755,0,0,0,1,1,1,0,19,genu of CC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_20,0.037000000000000005,-37.6845,6.14675,0,0,0,1,1,1,0,20,splenium of CC,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_21,34.312250000000006,-4.982,-26.87875,0,0,0,1,1,1,0,21,R AL temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_22,-34.72725,-7.2475,-25.203,0,0,0,1,1,1,0,22,L AL temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_23,18.69625,-10.56775,-17.7725,0,0,0,1,1,1,0,23,R superior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_24,-20.12075,-11.62125,-17.1495,0,0,0,1,1,1,0,24,L superior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_25,21.07325,-4.56975,-28.90925,0,0,0,1,1,1,0,25,R inferior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_26,-21.966749999999998,-5.28875,-27.895,0,0,0,1,1,1,0,26,L inferior AM temporal horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_27,14.40775,-39.697250000000004,3.8390000000000004,0,0,0,1,1,1,0,27,R indusium griseum origin,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_28,-15.48075,-42.28375,3.9659999999999997,0,0,0,1,1,1,0,28,L indusium griseum origin,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_29,20.730249999999998,-79.47475,4.85125,0,0,0,1,1,1,0,29,R ventral occipital horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_30,-19.41825,-81.46925,3.785,0,0,0,1,1,1,0,30,L ventral occipital horn,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_31,12.108500000000001,17.02725,-12.94,0,0,0,1,1,1,0,31,R olfactory sulcal fundus,vtkMRMLScalarVolumeNode1
+vtkMRMLMarkupsFiducialNode_32,-13.34325,17.0885,-13.35225,0,0,0,1,1,1,0,32,L olfactory sulcal fundus,vtkMRMLScalarVolumeNode1

afids_utils/tests/test_io.py

@@ -0,0 +1,122 @@
+from __future__ import annotations
+
+import csv
+import tempfile
+from os import PathLike, remove
+from pathlib import Path
+
+import numpy as np
+import pytest
+from hypothesis import HealthCheck, assume, given, settings
+from hypothesis import strategies as st
+from hypothesis.extra.numpy import arrays
+from numpy.typing import NDArray
+
+from afids_utils.exceptions import InvalidFiducialNumberError
+from afids_utils.io import FCSV_FIELDNAMES, afids_to_fcsv, get_afid
+
+
+@pytest.fixture
+def valid_fcsv_file() -> PathLike[str]:
+    return (
+        Path(__file__).parent / "data" / "tpl-MNI152NLin2009cAsym_afids.fcsv"
+    )
+
+
+class TestGetAfid:
+    @given(afid_num=st.integers(min_value=1, max_value=32))
+    @settings(
+        suppress_health_check=[HealthCheck.function_scoped_fixture],
+    )
+    def test_valid_num_get_afid(
+        self, valid_fcsv_file: PathLike[str], afid_num: int
+    ):
+        afid = get_afid(valid_fcsv_file, afid_num)
+
+        # Check array type
+        assert isinstance(afid, np.ndarray)
+        # Check array values
+        assert afid.dtype == np.single
+
+    @given(afid_num=st.integers(min_value=-1000, max_value=1000))
+    @settings(
+        suppress_health_check=[HealthCheck.function_scoped_fixture],
+    )
+    def test_invalid_num_get_afid(
+        self,
+        valid_fcsv_file: PathLike[str],
+        afid_num: int,
+    ):
+        assume(afid_num < 1 or afid_num > 32)
+
+        with pytest.raises(
+            InvalidFiducialNumberError, match=".*is not valid."
+        ):
+            get_afid(valid_fcsv_file, afid_num)
+
+
+@st.composite
+def afid_coords(
+    draw: st.DrawFn,
+    min_value: float = -50.0,
+    max_value: float = 50.0,
+    width: int = 16,
+) -> NDArray[np.single]:
+    coords = draw(
+        arrays(
+            shape=(32, 3),
+            dtype=np.single,
+            elements=st.floats(
+                min_value=min_value, max_value=max_value, width=width
+            ),
+        )
+    )
+
+    return coords
+
+
+class TestAfidsToFcsv:
+    @given(afids_coords=afid_coords())
+    @settings(
+        suppress_health_check=[HealthCheck.function_scoped_fixture],
+    )
+    def test_write_fcsv(
+        self, afids_coords: NDArray[np.single], valid_fcsv_file: PathLike[str]
+    ) -> None:
+        out_fcsv_file = tempfile.NamedTemporaryFile(
+            mode="w", delete=False, prefix="sub-test_afids.fcsv"
+        )
+        out_fcsv_path = Path(out_fcsv_file.name)
+
+        afids_to_fcsv(afids_coords, out_fcsv_path)
+
+        # Check file was created
+        assert out_fcsv_path.exists()
+
+        # Load files
+        with open(
+            valid_fcsv_file, "r", encoding="utf-8", newline=""
+        ) as template_fcsv_file:
+            template_header = [template_fcsv_file.readline() for _ in range(3)]
+
+        with open(
+            out_fcsv_path, "r", encoding="utf-8", newline=""
+        ) as output_fcsv_file:
+            output_header = [output_fcsv_file.readline() for _ in range(3)]
+            reader = csv.DictReader(
+                output_fcsv_file, fieldnames=FCSV_FIELDNAMES
+            )
+            output_fcsv = list(reader)
+
+        # Check header
+        assert output_header == template_header
+        # Check contents
+        for idx, row in enumerate(output_fcsv):
+            assert (row["x"], row["y"], row["z"]) == (
+                str(afids_coords[idx][0]),
+                str(afids_coords[idx][1]),
+                str(afids_coords[idx][2]),
+            )
+
+        # Delete temporary file
+        remove(out_fcsv_path)

codecov.yml

@@ -0,0 +1,16 @@
+comment:
+  layout: "header, diff, flags, components"
+
+coverage:
+  status:
+    project:
+      default:
+        target: 100%
+        threshold: 5%
+
+component_management:
+  individual_components:
+    - component_id: afids-utils_io
+      name: afids-utils_io
+      paths:
+        - afids_utils/io/