From 0e02565c95fbb317e8cc84126cfb70aa84b5557e Mon Sep 17 00:00:00 2001
From: Matthew Kerr <matthew.kerr@nrl.navy.mil>
Date: Thu, 15 Dec 2022 14:09:54 -0500
Subject: [PATCH 1/2] Fix numerical slop reading in ASCII profiles, add tests.

---
 src/pint/templates/lcfitters.py  |  3 +++
 src/pint/templates/lctemplate.py | 46 +++++++++++++++++++++++++-------
 tests/test_templates.py          | 38 ++++++++++++++++++++++++++
 3 files changed, 77 insertions(+), 10 deletions(-)

diff --git a/src/pint/templates/lcfitters.py b/src/pint/templates/lcfitters.py
index 073a5be96..bd5cd4d53 100644
--- a/src/pint/templates/lcfitters.py
+++ b/src/pint/templates/lcfitters.py
@@ -405,6 +405,9 @@ def fit_position(self, unbinned=True, track=False, skip_coarse=False):
 
         """
 
+        if not self.template.check_bounds():
+            raise ValueError("Template does not satisfy parameter bounds.")
+
         self._set_unbinned(unbinned)
         ph0 = self.template.get_location()
 
diff --git a/src/pint/templates/lctemplate.py b/src/pint/templates/lctemplate.py
index cef2e5fb9..db2a92de5 100644
--- a/src/pint/templates/lctemplate.py
+++ b/src/pint/templates/lctemplate.py
@@ -1029,7 +1029,7 @@ def gradient(self, parameters):
         return rvals
 
 
-def prim_io(template):
+def prim_io(template, bound_eps=1e-5):
     """Read files and build LCPrimitives."""
 
     def read_gaussian(toks):
@@ -1047,15 +1047,41 @@ def read_gaussian(toks):
                 g.errors[0] = float(tok[4]) / 2.3548200450309493
             elif tok[0].startswith("ampl"):
                 norms.append(float(tok[2]))
-        return primitives, norms
-
-    toks = [line.strip().split() for line in open(template) if len(line.strip()) > 0]
-    if "gauss" in toks[0]:
-        return read_gaussian(toks[1:])
-    elif "kernel" in toks[0]:
-        return [LCKernelDensity(input_file=toks[1:])], None
-    elif "fourier" in toks[0]:
-        return [LCEmpiricalFourier(input_file=toks[1:])], None
+        # check to that bounds are OK
+        for iprim, prim in enumerate(primitives):
+            if prim.check_bounds():
+                continue
+            for ip, p in enumerate(prim.p):
+                lo, hi = prim.bounds[ip]
+                if (p < lo) and (abs(p - lo) < bound_eps):
+                    prim.p[ip] = lo
+                if (p > hi) and (abs(p - hi) < bound_eps):
+                    prim.p[ip] = hi
+            if not prim.check_bounds():
+                raise ValueError("Unrecoverable bounds errors on input.")
+        # check norms
+        norms = np.asarray(norms)
+        n = norms.sum()
+        if (n > 1) and (abs(n - 1) < bounds_eps):
+            norms *= 1.0 / n
+        return primitives, list(norms)
+
+    lines = None
+    try:
+        with open(template, "r") as f:
+            lines = f.readlines()
+    except FileNotFoundError:
+        lines = template.split("\n")
+    if lines is None:
+        raise ValueError("Could not load lines from template.")
+    toks = [line.strip().split() for line in lines if len(line.strip()) > 0]
+    label, toks = toks[0], toks[1:]
+    if "gauss" in label:
+        return read_gaussian(toks)
+    elif "kernel" in label:
+        return [LCKernelDensity(input_file=toks)], None
+    elif "fourier" in label:
+        return [LCEmpiricalFourier(input_file=toks)], None
     raise ValueError("Template format not recognized!")
 
 
diff --git a/tests/test_templates.py b/tests/test_templates.py
index 35713aec1..596097e6e 100644
--- a/tests/test_templates.py
+++ b/tests/test_templates.py
@@ -43,6 +43,32 @@ def test_prim_gauss_definition():
     assert abs(g1(0.48) - expected_val) < 1e-6
 
 
+def test_prim_io():
+    """Test functionality to save a template and have it obey founds."""
+    # This will fail unless we use loose bounds checking
+    template1 = """
+    # gauss
+    -------------------------
+    const = 0.95915 +/- 0.00000
+    phas1 = 0.00000 +/- 0.00000
+    fwhm1 = 0.02514 +/- 0.00000
+    ampl1 = 0.03810 +/- 0.00000
+    phas2 = 0.53059 +/- 0.00000
+    fwhm2 = 0.01177 +/- 0.00000
+    ampl2 = 0.00275 +/- 0.00000
+    -------------------------
+    """
+    with pytest.raises(ValueError):
+        prims, norms = lctemplate.prim_io(template1, bound_eps=0)
+
+    # this should work and set the lower bound to 0.005
+    prims, norms = lctemplate.prim_io(template1)
+    assert prims[1].p[0] == prims[1].bounds[0][0]
+
+    template2 = template1.replace("1177", "1178")
+    prims, norms = lctemplate.prim_io(template2)
+
+
 def test_prim_gauss_wrapping():
 
     # default is to wrap a function by 10 times; make a fat pulse here and
@@ -465,6 +491,18 @@ def test_simple_fit_unbinned():
 """
     assert expected_val.strip() == str(lcf).strip()
 
+    # check position fitting
+    offset, error = lcf.fit_position()
+    assert abs(offset < 1e-7)
+    assert abs(error - 0.00055513) < 1e-7
+
+    # check that fitting with a bad parameter boundary fails
+    p = lcf.template.primitives[0]
+    p.p[0] = p.bounds[0][0] - 1e-4
+    assert not (p.check_bounds())
+    with pytest.raises(ValueError):
+        lcf.fit_position()
+
 
 def test_simple_fit_binned():
     """Make sure objects adequately implement mathematical intent."""

From 4351d8f91539667243baae0a8dafcf6f54695a23 Mon Sep 17 00:00:00 2001
From: Matthew Kerr <matthew.kerr@nrl.navy.mil>
Date: Thu, 15 Dec 2022 17:44:22 -0500
Subject: [PATCH 2/2] Add to CHANGELOG.

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d77700bfc..da95c9607 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project, at least loosely, adheres to [Semantic Versioning](https://sem
 ### Added
 - method to identify mask parameters with no TOAs and optionally freeze them
 ### Fixed
+- corrected a precision issue with reading ASCII representations of pulse profiles
 ### Removed
 - termios import for solar_wind_dispersion