Merge pull request #17 from pheuer/coverage_improvements

Coverage improvements

src/cr39py/core/ci.py

@@ -6,7 +6,7 @@
 from matplotlib import use as matplotlib_use
 
 
-def in_ci():
+def in_ci():  # pragma: no cover
     """
     GitLab CI sets the variable CI == 'true' on all pipelines,
     so the presence and value of this environment variable can be used
@@ -15,15 +15,15 @@ def in_ci():
     return "CI" in os.environ and os.environ["CI"] == "true"
 
 
-def in_unit_test():
+def in_unit_test():  # pragma: no cover
     """
     Pytest sets this environment variable
     """
     # https://stackoverflow.com/questions/25188119/test-if-code-is-executed-from-within-a-py-test-session
     return "PYTEST_CURRENT_TEST" in os.environ
 
 
-class SilentPlotting:
+class SilentPlotting:  # pragma: no cover
     """
     Context manager that allows matplotlib to create plots silently
     to ensure plotting functions run without actually having all the plots

src/cr39py/etch/tools.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 
-def goal_diameter(fluence, desired_F2=0.05, max_goal=10):
+def goal_diameter(fluence, desired_F2=0.025, max_goal=10):
     """Calculates the ideal track diameter in um to achieve a given overlap parameter F2.
 
     Parameters
@@ -13,8 +13,8 @@ def goal_diameter(fluence, desired_F2=0.05, max_goal=10):
 
     desired_F2 : float, optional
         The desired track overlap parameter F2. The default
-        value is 0.05, meaning that ~5% of tracks will suffer overlap with
-        a neighbor.
+        value is 0.025, meaning that ~2.5% of tracks will suffer overlap with
+        a neighbor. The model breaks down for F2~>0.3.
 
     max_goal : float, optional
         A maximum at which the goal track diameter will be clipped, in um.
@@ -24,6 +24,13 @@ def goal_diameter(fluence, desired_F2=0.05, max_goal=10):
     -------
     goal_diameter: float
         The goal track diameter in um.
+
+
+    Raises
+    ------
+    ValueError
+        If desired_F2 > 0.3, in which case the model breaks down.
+
     """
 
     def chi(F2):

src/cr39py/scan/base_scan.py

@@ -59,10 +59,10 @@ def __init__(
         parent_scan: "Scan" = None,
     ) -> None:
 
-        if ind is None:
+        if ind is None:  # pragma: no cover
             raise ValueError("ind argument is required")
 
-        if unit is None:
+        if unit is None:  # pragma: no cover
             raise ValueError("unit argument is required")
 
         # These parameters are intended to not be mutable
@@ -249,6 +249,8 @@ def __init__(self) -> None:
         # Etch time, u.Quantity
         self._etch_time = None
 
+        self._filepath = None
+
         self.metadata = {}
 
     @property
@@ -278,6 +280,16 @@ def etch_time(self) -> u.Quantity:
         """
         return self._etch_time
 
+    @property
+    def filepath(self) -> Path:
+        """
+        Path to the file from which the scan was loaded.
+
+        If the scan was not loaded from a file, e.g. if it was
+        created directly from a track array, this will be ``None``.
+        """
+        return self._filepath
+
     @property
     def axes(self) -> dict[Axis]:
         """
@@ -350,7 +362,10 @@ def from_cpsa(cls, path: Path, etch_time: float | None = None):
 
         tracks, metadata = read_cpsa(path)
 
-        return cls.from_tracks(tracks, etch_time, metadata=metadata)
+        obj = cls.from_tracks(tracks, etch_time, metadata=metadata)
+        obj._filepath = path
+
+        return obj
 
     # **********************************
     # Framesize setup
@@ -944,6 +959,16 @@ def save_histogram(self, path: Path, *args, **kwargs) -> None:
         elif ext.lower() == ".csv":
             np.savetxt(path, arr.m, delimiter=",")
 
+        elif ext.lower() == ".png":
+            fig, ax = plt.subplots()
+            ax.set_aspect("equal")
+            if self.filepath is not None:
+                ax.set_title(self.filepath.stem, fontsize=9)
+            ax.pcolormesh(hax.m, vax.m, arr.m.T)
+            ax.set_xlabel("X")
+            ax.set_ylabel("Y")
+            fig.savefig(path, dpi=200)
+
         else:
             raise ValueError(f"Unsupported file extension: {ext}")
 

src/cr39py/scan/cpsa.py

@@ -272,6 +272,7 @@ def extract_etch_time(path: Path) -> float:
         returns None.
 
     """
+    path = Path(path)
 
     # Cast the filename as lowercase, so "H" and "h" will both match
     filename = str(path.name).lower()

src/cr39py/scan/cut.py

@@ -234,28 +234,31 @@ def test(self, trackdata):
         """
         Returns a boolean array representing which tracks fall within this cut.
 
+        Note that the mask returned by this function is tracks that are inside
+        the cut, e.g. tracks that should be excluded by the cut.
+
         Parameters
         ----------
         trackdata : np.ndarray (ntracks, 6)
             Track data array.
 
         Returns
         -------
-        keep : np.ndarray, bool (ntracks,)
+        in_cut : np.ndarray, bool (ntracks,)
             A boolean array indicating whether or not each track in the
             trackdata array fits within the cut.
 
         """
         ntracks, _ = trackdata.shape
-        keep = np.ones(ntracks).astype("bool")
+        in_cut = np.ones(ntracks).astype("bool")
 
         for key in self.bounds.keys():
             if self.bounds[key] is not None:
                 i = self.indices[key]
                 if "min" in key:
-                    keep *= np.greater(trackdata[:, i], getattr(self, key))
+                    in_cut *= np.greater(trackdata[:, i], getattr(self, key))
                 else:
-                    keep *= np.less(trackdata[:, i], getattr(self, key))
+                    in_cut *= np.less(trackdata[:, i], getattr(self, key))
 
         # Return a 1 for every track that is in the cut
-        return keep.astype(bool)
+        return in_cut.astype(bool)

src/cr39py/scan/subset.py

@@ -18,8 +18,6 @@
 from cr39py.core.types import TrackData
 from cr39py.scan.cut import Cut
 
-# TODO: Eliminate the domain? Why not just have that be another cut in the cut list...
-
 
 class Subset(ExportableClassMixin):
     """
@@ -28,6 +26,9 @@ class Subset(ExportableClassMixin):
     The subset is defined by a domain, a list
     of cuts, and a number of diameter slices (Dslices).
 
+    The domain is a cut that defines the area in parameter space that the subset. Unlike regular cuts,
+    the domain is inclusive, and the ``apply_cuts`` method will not invert the domain when it inverts other cuts.
+
     Parameters
     ----------
 
@@ -134,10 +135,7 @@ def set_domain(self, *args, **kwargs) -> None:
             domain.
 
         """
-
-        if len(args) < 1 or args[0] is None:
-            self.domain = Cut()
-        elif len(args) == 1:
+        if len(args) == 1 and isinstance(args[0], Cut):
             c = args[0]
         else:
             c = Cut(**kwargs)
@@ -248,14 +246,19 @@ def remove_cut(self, i: int) -> None:
         i : int
             Index of the cut to remove
 
+        Raises
+        ------
+
+        ValueError
+            If the index is out of bounds.
+
         """
 
         if i > len(self.cuts) - 1:
-            print(
+            raise ValueError(
                 f"Cannot remove the {i} cut, there are only " f"{len(self.cuts)} cuts."
             )
-        else:
-            self.cuts.pop(i)
+        self.cuts.pop(i)
 
     def replace_cut(self, i: int, cut: Cut):
         """Replace the ith cut in the Subset list with a new cut
@@ -266,13 +269,19 @@ def replace_cut(self, i: int, cut: Cut):
             Index of the Cut to replace.
         cut : `~cr39py.cut.Cut`
             New cut to insert.
+
+        Raises
+        ------
+
+        ValueError
+            If the index is out of bounds.
+
         """
         if i > len(self.cuts) - 1:
-            print(
+            raise ValueError(
                 f"Cannot replace the {i} cut, there are only " f"{len(self.cuts)} cuts."
             )
-        else:
-            self.cuts[i] = cut
+        self.cuts[i] = cut
 
     def apply_cuts(
         self, tracks: TrackData, use_cuts: list[int] | None = None, invert: bool = False
@@ -292,8 +301,8 @@ def apply_cuts(
 
         invert : bool (optional)
             If True, return the inverse of the cuts selected, i.e. the
-            tracks that would otherwise be excluded. The default is
-            False.
+            tracks that would otherwise be excluded. The domain will not be inerted.
+            The default is False.
 
         Returns
         -------
@@ -331,16 +340,15 @@ def apply_cuts(
                 # in the excluded region
                 include *= np.logical_not(x)
 
-        # Regardless of anything else, only show tracks that are within
-        # the domain
         if self.domain is not None:
-            include *= self.domain.test(tracks)
+            domain_include = self.domain.test(tracks)
 
-        # Select only these tracks
+        # Select only these these tracks
+        # If inverting, do not invert the domain tracks
         if invert:
-            selected_tracks = tracks[~include, :]
+            selected_tracks = tracks[(~include) * domain_include, :]
         else:
-            selected_tracks = tracks[include, :]
+            selected_tracks = tracks[include * domain_include, :]
 
         # Calculate the bin edges for each dslice
         # !! note that the tracks are already sorted into order by diameter

tests/etch/test_tools.py

@@ -0,0 +1,27 @@
+"""_
+This file contains tests for the etch/tools.py file.
+"""
+
+import numpy as np
+import pytest
+
+from cr39py.etch.tools import goal_diameter
+
+cases = [
+    (1e5, 0.05, 20, 4.06),
+    # Extremely low fluence and high F2 to test max goal diameter
+    (1e2, 0.2, 5, 5),
+]
+
+
+@pytest.mark.parametrize("fluence, desired_F2, max_goal, expected", cases)
+def test_goal_diameter(fluence, desired_F2, max_goal, expected):
+    assert np.isclose(goal_diameter(fluence, desired_F2, max_goal), expected, rtol=0.03)
+
+
+def test_goal_diameter_raises():
+    """
+    Raise an exception if F2 > 0.3
+    """
+    with pytest.raises(ValueError):
+        goal_diameter(1e5, 0.4, 20)

tests/scan/test_scan.py → tests/scan/test_base_scan.py

@@ -62,15 +62,38 @@ def test_subset(cr39scan):
     with pytest.raises(ValueError):
         cr39scan.remove_subset(0)
 
-    cr39scan.remove_subset(2)
+    # Cannot select subset outside range
+    with pytest.raises(ValueError):
+        cr39scan.remove_subset(1000)
+
+    # Select the last tubset
+    cr39scan.select_subset(-1)
+
+    # Remove the first subset
+    cr39scan.remove_subset(0)
+
+
+def test_manipulate_cuts(cr39scan):
+
+    cr39scan.set_domain(xmin=0)
+    cr39scan.add_cut(cmin=30)
+    cr39scan.add_cut(Cut(dmin=10))
+
+    cr39scan.set_ndslices(2)
+    cr39scan.select_dslice(0)
+
+    cr39scan.remove_cut(1)
+    cr39scan.replace_cut(0, Cut(cmin=20))
 
 
 @pytest.mark.parametrize("statistic", ["mean", "median"])
 def test_track_energy(cr39scan, statistic):
     cr39scan.track_energy("D", statistic)
 
 
-@pytest.mark.parametrize("attribute", ["chi", "F2", "track_density"])
+@pytest.mark.parametrize(
+    "attribute", ["chi", "F2", "track_density", "etch_time", "ntracks"]
+)
 def test_access_attributes(cr39scan, attribute):
     assert hasattr(cr39scan, attribute)
     getattr(cr39scan, attribute)
@@ -84,21 +107,19 @@ def test_histogram(cr39scan):
     cr39scan.histogram()
 
 
-def test_plot(cr39scan):
+@pytest.mark.parametrize("fcn_name", ["cutplot", "plot", "focus_plot"])
+def test_plot_functions(fcn_name, cr39scan):
     with SilentPlotting():
-        cr39scan.cutplot()
+        getattr(cr39scan, fcn_name)()
 
 
-@pytest.mark.parametrize("ext", [".csv", ".h5"])
+@pytest.mark.parametrize("ext", [".csv", ".h5", ".png"])
 def test_save_histogram(cr39scan, tmp_path, ext):
 
     # Save the histogram
     path = tmp_path / Path("test_histogram" + ext)
     cr39scan.save_histogram(path)
 
-    # Get the histogram for reference
-    _, _, hist = cr39scan.histogram()
-
     # Read the data from the histogram
     if ext == ".h5":
         with h5py.File(path, "r") as f:
@@ -107,5 +128,12 @@ def test_save_histogram(cr39scan, tmp_path, ext):
     elif ext == ".csv":
         data = np.loadtxt(path, delimiter=",")
 
+    elif ext == ".png":
+        # Skip the check on the data in this case
+        return
+
+    # Get the histogram for reference
+    _, _, hist = cr39scan.histogram()
+
     # Test that the data matches expectations
     assert np.allclose(data, hist, rtol=0.05)