Merge branch 'main' into filtration_stacks

README.md

@@ -1,4 +1,8 @@
-# CR39py
-Code for analyzing CR39 particle track data
+# cr39py
+[![codecov](https://codecov.io/gh/pheuer/cr39py/branch/main/graph/badge.svg?token=K0JA0QCH3S)](https://codecov.io/gh/pheuer/cr39py)
+![ci workflow](https://github.com/pheuer/cr39py/actions/workflows/ci.yml/badge.svg)
+![rtd](https://readthedocs.org/projects/cr39py/badge/?version=latest&style=flat)
+
+Code for designing experiments using CR-39, calculating etch times for CR-39 processing, and analyzing CR-39 track data.
 
 Documentation: https://cr39py.readthedocs.io/en/latest/

docs/source/notebooks/nuclear_reaction_data.ipynb

@@ -7,9 +7,16 @@
     "# Estimating proton yields from nTOF measurements"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Note: because of how ReadTheDocs works, this notebook is pre-executed"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,7 +35,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
@@ -52,7 +59,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
@@ -106,19 +113,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 12,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "D3He Yield: 4.48e+07, Yield ratio: 0.45\n"
+     ]
+    }
+   ],
    "source": [
     "D_pressure = 6.5*u.atm\n",
     "He_pressure = 13*u.atm\n",
     "DDn_yield = 1e8\n",
     "Tion = 11 * u.keV\n",
-    "D3He_proton_yield = d3hep_yield(DDn_yield D_pressure, He_pressure, Tion)\n",
+    "D3He_proton_yield = d3hep_yield(DDn_yield, D_pressure, He_pressure, Tion)\n",
     "yield_ratio = D3He_proton_yield/DDn_yield\n",
-    "print(f\"D3He Yield: {D3He_proton_yield:.2e}, Yield ratio: {yratio:.2f}\")"
+    "print(f\"D3He Yield: {D3He_proton_yield:.2e}, Yield ratio: {yield_ratio:.2f}\")"
    ]
-  }],
+  }
+ ],
  "metadata": {
   "kernelspec": {
    "display_name": "dev312",

src/cr39py/core/ci.py

@@ -32,7 +32,7 @@ class SilentPlotting:
 
     def __enter__(self):
         warnings.filterwarnings(
-            "ignore", message="FigureCanvasAgg", category=UserWarning
+            "ignore", "FigureCanvasAgg is non-interactive, and thus cannot be shown"
         )
         self.current_backend = get_backend()
         plt.close("all")
@@ -41,4 +41,3 @@ def __enter__(self):
     def __exit__(self, exc_type, exc_val, exc_tb):
         plt.close("all")
         matplotlib_use(self.current_backend)
-        warnings.resetwarnings()

src/cr39py/scan/base_scan.py

@@ -240,6 +240,8 @@ def __init__(self) -> None:
         # Etch time, u.Quantity
         self._etch_time = None
 
+        self.metadata = {}
+
     @property
     def tracks(self) -> TrackData:
         """
@@ -281,7 +283,9 @@ def axes(self) -> dict[Axis]:
     # **********************************
 
     @classmethod
-    def from_tracks(cls, tracks: TrackData, etch_time: float):
+    def from_tracks(
+        cls, tracks: TrackData, etch_time: float, metadata: dict | None = None
+    ):
         """
         Initialize a Scan object from an array of tracks.
 
@@ -292,11 +296,18 @@ def from_tracks(cls, tracks: TrackData, etch_time: float):
 
         etch_time : float
             Etch time in minutes.
+
+        metadata : dict
+            Dictionary of metadata to attach to the Scan object.
         """
         obj = cls()
 
+        if metadata is None:
+            metadata = {}
+
         obj._etch_time = etch_time * u.min
         obj._tracks = tracks
+        obj.metadata = metadata
 
         # Attach the selected tracks object to the axes objects
         for ax in obj._axes.values():
@@ -309,6 +320,10 @@ def from_cpsa(cls, path: Path, etch_time: float | None = None):
         """
         Initialize a Scan object from a CPSA file.
 
+        The etch_time can be automatically extracted from the filename
+        if it is included in a format like  ``_#m_``, ``_#min_``, ``_#h_``,
+        ``_#hr_``, etc.
+
         Parameters
         ---------
         path : `~pathlib.Path`
@@ -318,16 +333,19 @@ def from_cpsa(cls, path: Path, etch_time: float | None = None):
             Etch time in minutes.
 
         """
+
+        # If the etch time is not provided, attempt to automatically extract
+        # from the CPSA filename
         if etch_time is None:
             etch_time = extract_etch_time(path)
         if etch_time is None:
             raise ValueError(
                 "Etch time not provided or successfully extracted from CPSA filename."
             )
 
-        tracks = read_cpsa(path)
+        tracks, metadata = read_cpsa(path)
 
-        return cls.from_tracks(tracks, etch_time)
+        return cls.from_tracks(tracks, etch_time, metadata=metadata)
 
     # **********************************
     # Framesize setup

src/cr39py/scan/cpsa.py

@@ -72,8 +72,22 @@ def read_cpsa(path: Path) -> TrackData:
         fy = pix_size * NFPy
         print(f"...Microscope frame size fx, fy: {fx:.1e} um, {fy:.1e} um")
 
-        # Read the full datafile as int32 and separate out the track info
+        # Store the scan data in a dictionary, which will be returned along with
+        # the track data
+        metadata = {
+            "version": version,
+            "nx_frames": nx,
+            "ny_frames": ny,
+            "nframes": nframes,
+            "pixel_size": pix_size,
+            "threshold": threshold,
+            "NFPx": NFPx,
+            "NFPy": NFPy,
+            "frame_size_x": fx,
+            "frame_size_y": fy,
+        }
 
+        # Read the full datafile as int32 and separate out the track info
         # Represents metadata from a single frame of cr39
         # used when reading CPSA files
         FrameHeader = namedtuple(
@@ -184,6 +198,16 @@ def read_cpsa(path: Path) -> TrackData:
 
             frame_tracks.append(t)
 
+        # Read the footer, save the whole string into the metadata
+        # This contains a bunch of additional metadata
+        footer = b""
+        for line in file:
+            footer += line
+        footer = footer.decode("cp1250")
+        metadata["cpsa_footer"] = footer
+
+    # CPSA file now closed - post-process the data
+
     # The order of the quantities in track data is:
     # 0) x position (cm))
     # 1) y position (cm)
@@ -205,7 +229,28 @@ def read_cpsa(path: Path) -> TrackData:
     # Sort the yaxis (it's backwards...)
     yax = np.sort(yax)
 
-    return tracks
+    # Extract some quantities from the footer using regex
+    # In scans that are part of a coincidence counting process, six marks will be made on the piece
+    # This regex pulls out the lines in the footer that record where these images were taken, which
+    # look like this
+    # IMAGES recorded before and after this scan were at:
+    #   0>    (4.22560, 2.76639)   [Notes: UL-m]
+    #   1>    (0.52671, 2.75683)   [Notes: UR-m]
+    #   2>    (4.27408, 2.76639)   [Notes: UL-FE]
+    #   3>    (0.48003, 2.75683)   [Notes: UR-NE]
+    #   4>    (4.53513, 2.76701)   [Notes: UL-NE]
+    #   5>    (0.74559, 2.75503)   [Notes: UR-FE]
+    note_fields = ["UL-m", "UR-m", "UL-FE", "UL-NE", "UR-FE", "UR-NE"]
+    for note in note_fields:
+        # This regex matches a line like "0>    (4.22560, 2.76639)   [Notes: UL-m]"
+        # and extracts the pair of points (4.22560, 2.76639) as the match group
+        pattern = f"\([+-]?([0-9]*[.][0-9]+),\s[+-]?([0-9]*[.][0-9]+)\)[\s]+\[Notes:[\s]+{note}\]\n"
+        match = re.search(pattern, footer)
+        if match is not None:
+            point = np.array([float(x) for x in match.groups()])
+            metadata[note] = point
+
+    return tracks, metadata
 
 
 def extract_etch_time(path: Path) -> float: