Changeset 275b07dc in sasmodels for explore

Timestamp:

Oct 30, 2018 10:28:33 AM (6 years ago)

Author:

GitHub <noreply@…>

Branches:

master, core_shell_microgels, magnetic_model, ticket-1257-vesicle-product, ticket_1156, ticket_1265_superball, ticket_822_more_unit_tests

Children:

c6084f1

Parents:

df87acf (diff), 57c609b (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Paul Kienzle <pkienzle@…> (10/30/18 10:28:33)

git-committer:

GitHub <noreply@…> (10/30/18 10:28:33)

Message:

Merge pull request #87 from SasView?/ticket-1074-gammainc

Add gammaln and gammainc to the opencl math library. Closes #1074.

File:

• explore/precision.py (modified) (10 diffs)

explore/precision.py

@@ -95 +95 @@
             neg:    [-100,100]
 
+        For arbitrary range use "start:stop:steps:scale" where scale is
+        one of log, lin, or linear.
+
         *diff* is "relative", "absolute" or "none"
 
@@ -102 +105 @@
         linear = not xrange.startswith("log")
         if xrange == "zoom":
-            lin_min, lin_max, lin_steps = 1000, 1010, 2000
+            start, stop, steps = 1000, 1010, 2000
         elif xrange == "neg":
-            lin_min, lin_max, lin_steps = -100.1, 100.1, 2000
+            start, stop, steps = -100.1, 100.1, 2000
         elif xrange == "linear":
-            lin_min, lin_max, lin_steps = 1, 1000, 2000
-            lin_min, lin_max, lin_steps = 0.001, 2, 2000
+            start, stop, steps = 1, 1000, 2000
+            start, stop, steps = 0.001, 2, 2000
         elif xrange == "log":
-            log_min, log_max, log_steps = -3, 5, 400
+            start, stop, steps = -3, 5, 400
         elif xrange == "logq":
-            log_min, log_max, log_steps = -4, 1, 400
+            start, stop, steps = -4, 1, 400
+        elif ':' in xrange:
+            parts = xrange.split(':')
+            linear = parts[3] != "log" if len(parts) == 4 else True
+            steps = int(parts[2]) if len(parts) > 2 else 400
+            start = float(parts[0])
+            stop = float(parts[1])
+
         else:
             raise ValueError("unknown range "+xrange)
@@ -121 +131 @@
             # value to x in the given precision.
             if linear:
-                lin_min = max(lin_min, self.limits[0])
-                lin_max = min(lin_max, self.limits[1])
-                qrf = np.linspace(lin_min, lin_max, lin_steps, dtype='single')
-                #qrf = np.linspace(lin_min, lin_max, lin_steps, dtype='double')
+                start = max(start, self.limits[0])
+                stop = min(stop, self.limits[1])
+                qrf = np.linspace(start, stop, steps, dtype='single')
+                #qrf = np.linspace(start, stop, steps, dtype='double')
                 qr = [mp.mpf(float(v)) for v in qrf]
-                #qr = mp.linspace(lin_min, lin_max, lin_steps)
+                #qr = mp.linspace(start, stop, steps)
             else:
-                log_min = np.log10(max(10**log_min, self.limits[0]))
-                log_max = np.log10(min(10**log_max, self.limits[1]))
-                qrf = np.logspace(log_min, log_max, log_steps, dtype='single')
-                #qrf = np.logspace(log_min, log_max, log_steps, dtype='double')
+                start = np.log10(max(10**start, self.limits[0]))
+                stop = np.log10(min(10**stop, self.limits[1]))
+                qrf = np.logspace(start, stop, steps, dtype='single')
+                #qrf = np.logspace(start, stop, steps, dtype='double')
                 qr = [mp.mpf(float(v)) for v in qrf]
-                #qr = [10**v for v in mp.linspace(log_min, log_max, log_steps)]
+                #qr = [10**v for v in mp.linspace(start, stop, steps)]
 
         target = self.call_mpmath(qr, bits=500)
@@ -176 +186 @@
     """
     if diff == "relative":
-        err = np.array([abs((t-a)/t) for t, a in zip(target, actual)], 'd')
+        err = np.array([(abs((t-a)/t) if t != 0 else a) for t, a in zip(target, actual)], 'd')
         #err = np.clip(err, 0, 1)
         pylab.loglog(x, err, '-', label=label)
@@ -197 +207 @@
     return model_info
 
+# Hack to allow second parameter A in two parameter functions
+A = 1
+def parse_extra_pars():
+    global A
+
+    A_str = str(A)
+    pop = []
+    for k, v in enumerate(sys.argv[1:]):
+        if v.startswith("A="):
+            A_str = v[2:]
+            pop.append(k+1)
+    if pop:
+        sys.argv = [v for k, v in enumerate(sys.argv) if k not in pop]
+        A = float(A_str)
+
+parse_extra_pars()
+
 
 # =============== FUNCTION DEFINITIONS ================
@@ -297 +324 @@
     ocl_function=make_ocl("return sas_gamma(q);", "sas_gamma", ["lib/sas_gamma.c"]),
     limits=(-3.1, 10),
+)
+add_function(
+    name="gammaln(x)",
+    mp_function=mp.loggamma,
+    np_function=scipy.special.gammaln,
+    ocl_function=make_ocl("return sas_gammaln(q);", "sas_gammaln", ["lib/sas_gammainc.c"]),
+    #ocl_function=make_ocl("return lgamma(q);", "sas_gammaln"),
+)
+add_function(
+    name="gammainc(x)",
+    mp_function=lambda x, a=A: mp.gammainc(a, a=0, b=x)/mp.gamma(a),
+    np_function=lambda x, a=A: scipy.special.gammainc(a, x),
+    ocl_function=make_ocl("return sas_gammainc(%.15g,q);"%A, "sas_gammainc", ["lib/sas_gammainc.c"]),
+)
+add_function(
+    name="gammaincc(x)",
+    mp_function=lambda x, a=A: mp.gammainc(a, a=x, b=mp.inf)/mp.gamma(a),
+    np_function=lambda x, a=A: scipy.special.gammaincc(a, x),
+    ocl_function=make_ocl("return sas_gammaincc(%.15g,q);"%A, "sas_gammaincc", ["lib/sas_gammainc.c"]),
 )
 add_function(
@@ -463 +509 @@
 lanczos_gamma = """\
     const double coeff[] = {
-            76.18009172947146,     -86.50532032941677,
-            24.01409824083091,     -1.231739572450155,
+            76.18009172947146, -86.50532032941677,
+            24.01409824083091, -1.231739572450155,
             0.1208650973866179e-2,-0.5395239384953e-5
             };
@@ -475 +521 @@
 """
 add_function(
-    name="log gamma(x)",
+    name="loggamma(x)",
     mp_function=mp.loggamma,
     np_function=scipy.special.gammaln,
@@ -599 +645 @@
 
 ALL_FUNCTIONS = set(FUNCTIONS.keys())
-ALL_FUNCTIONS.discard("loggamma")  # OCL version not ready yet
+ALL_FUNCTIONS.discard("loggamma")  # use cephes-based gammaln instead
 ALL_FUNCTIONS.discard("3j1/x:taylor")
 ALL_FUNCTIONS.discard("3j1/x:trig")
@@ -615 +661 @@
     -r indicates that the relative error should be plotted (default),
     -x<range> indicates the steps in x, where <range> is one of the following
-      log indicates log stepping in [10^-3, 10^5] (default)
-      logq indicates log stepping in [10^-4, 10^1]
-      linear indicates linear stepping in [1, 1000]
-      zoom indicates linear stepping in [1000, 1010]
-      neg indicates linear stepping in [-100.1, 100.1]
-and name is "all" or one of:
+        log indicates log stepping in [10^-3, 10^5] (default)
+        logq indicates log stepping in [10^-4, 10^1]
+        linear indicates linear stepping in [1, 1000]
+        zoom indicates linear stepping in [1000, 1010]
+        neg indicates linear stepping in [-100.1, 100.1]
+        start:stop:n[:stepping] indicates an n-step plot in [start, stop]
+            or [10^start, 10^stop] if stepping is "log" (default n=400)
+Some functions (notably gammainc/gammaincc) have an additional parameter A
+which can be set from the command line as A=value.  Default is A=1.
+
+Name is one of:
     """+names)
     sys.exit(1)