Merge pull request #16 from pheuer/prms_edits

New features to support PRMs (new PR)

docs/source/notebooks/filtration_stacks.ipynb

@@ -16,15 +16,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "import matplotlib.pyplot as plt\n",
     "\n",
     "from cr39py.core.units import u\n",
     "from cr39py.filtration.srim import SRIMData\n",
-    "from cr39py.filtration.stack import Layer, Stack"
+    "from cr39py import Layer, Stack"
    ]
   },
   {
@@ -40,7 +40,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 2,
    "metadata": {
     "tags": [
      "nbsphinx-thumbnail"
@@ -105,7 +105,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
@@ -133,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -164,7 +164,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -199,7 +199,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {

src/cr39py/__init__.py

@@ -1,4 +1,5 @@
-from cr39py.filtration.stack import Layer, Stack
+from cr39py.filtration.layer import Layer
+from cr39py.filtration.stack import Stack
 from cr39py.scan.base_scan import Scan
 from cr39py.scan.cut import Cut
 from cr39py.scan.subset import Subset

src/cr39py/etch/__init__.py

@@ -0,0 +1 @@
+"""The `~cr39py.etch` module contains functionality relating to the process of etching CR-39."""

src/cr39py/etch/tools.py

@@ -0,0 +1,41 @@
+"""The `~cr39py.etch.tools` module contains tools for calculating etch times."""
+
+import numpy as np
+
+
+def goal_diameter(fluence, desired_F2=0.05, max_goal=10):
+    """Calculates the ideal track diameter in um to achieve a given overlap parameter F2.
+
+    Parameters
+    ----------
+    fluence : float
+        The fluence on the CR-39 in 1/cm^2
+
+    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.
+
+    max_goal : float, optional
+        A maximum at which the goal track diameter will be clipped, in um.
+        Prevents extremely large goal diameters being suggested at low fluences.
+
+    Returns
+    -------
+    goal_diameter: float
+        The goal track diameter in um.
+    """
+
+    def chi(F2):
+        """
+        Zylstra Eq. 9 inverted to solve for chi given F2
+        Works up to F2=0.375, then the sqrt becomes imaginary.
+        """
+        return 3 / 4 * (1 - np.sqrt(1 - 8 / 3 * F2))
+
+    if desired_F2 > 0.3:
+        raise ValueError(f"Model breaks down for F2~>0.3, provided F2={desired_F2}")
+
+    goal_chi = chi(desired_F2)
+    goal_d = np.sqrt(goal_chi / np.pi / (fluence * 1e-8))
+    return np.clip(goal_d, a_min=0, a_max=max_goal)