Merge pull request jjhelmus#16 from tjragan/pipe_fix

jjhelmus · jjhelmus · commit e7e8ec3b114d · 2014-05-16T11:04:27.000-05:00
BUG: Two NMRPipe related fixes.
diff --git a/nmrglue/process/pipe_proc.py b/nmrglue/process/pipe_proc.py
@@ -2033,7 +2033,7 @@ def ext(dic, data, x1="default", xn="default", y1="default", yn="default",
         data = data[y_min:y_max, x_min:x_max]
         if y_min != 1 and y_max != data.shape[0]:  # only update when sliced
             dic["FDSLICECOUNT"] = y_max - y_min
-        dic["FDSPECNUM"] = y_max - y_min
+            dic["FDSPECNUM"] = y_max - y_min
         dic["FDSIZE"] = x_max - x_min
 
     else:       # 1D Array
diff --git a/nmrglue/util/misc.py b/nmrglue/util/misc.py
@@ -11,7 +11,7 @@
 
 
 def pair_similar(dic1, data1, dic2, data2, verb=False, atol=ATOL, rtol=RTOL,
-                 dtol=DTOL):
+                 dtol=DTOL, ignore_pipe_display=False):
     """
     Check a dic, data pair against a second dic, data pair for differences.
 
@@ -41,7 +41,8 @@ def pair_similar(dic1, data1, dic2, data2, verb=False, atol=ATOL, rtol=RTOL,
 
     """
     r1 = isdatasimilar(data1, data2, verb, atol, rtol)
-    r2 = isdicsimilar(dict(dic1), dict(dic2), verb, dtol)
+    r2 = isdicsimilar(dict(dic1), dict(dic2), verb, dtol, 
+                      ignore_pipe_display=ignore_pipe_display)
     return r1, r2
 
 
@@ -124,7 +125,7 @@ def isitemsimilar(v1, v2, verb=False, dtol=DTOL):
     return r
 
 
-def isdicsimilar(dic1, dic2, verb=False, dtol=DTOL):
+def isdicsimilar(dic1, dic2, verb=False, dtol=DTOL, ignore_pipe_display=False):
     """
     Compare two dictionaries for differences
 
@@ -161,6 +162,13 @@ def isdicsimilar(dic1, dic2, verb=False, dtol=DTOL):
     kset2 = set(dic2.keys())
     dset = set.difference(kset1, kset2)
     iset = set.intersection(kset1, kset2)
+    
+    if ignore_pipe_display == True:
+        iset.discard('FDMIN')
+        iset.discard('FDMAX')
+        iset.discard('FDDISPMIN')
+        iset.discard('FDDISPMAX')
+        iset.discard('FDSCALEFLAG')
 
     # print out any keys not in both dictionaries
     if len(dset) != 0:
diff --git a/tests/pipe_proc_tests/ext.com b/tests/pipe_proc_tests/ext.com
@@ -27,3 +27,33 @@ nmrPipe -in ./time_complex.fid                \
 nmrPipe -in ./time_complex.fid                \
 | nmrPipe  -fn EXT -x1 5 -xn 200 -round 10 -sw \
 -ov -out ext7.dat
+
+
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT -auto \
+-ov -out time-freq.c.ft1
+
+nmrPipe -in ./time-freq.c.ft1                \
+| nmrPipe  -fn EXT -left -sw\
+-ov -out ext8.dat
+
+nmrPipe -in ./time-freq.c.ft1                \
+| nmrPipe  -fn EXT -right -sw\
+-ov -out ext9.dat
+
+rm -f time-freq.c.ft1
+
+
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT -auto -di \
+-ov -out time-freq.r.ft1
+
+nmrPipe -in ./time-freq.r.ft1                \
+| nmrPipe  -fn EXT -left -sw\
+-ov -out ext10.dat
+
+nmrPipe -in ./time-freq.r.ft1                \
+| nmrPipe  -fn EXT -right -sw\
+-ov -out ext11.dat
+
+rm -f time-freq.r.ft1
diff --git a/tests/pipe_proc_tests/ext.py b/tests/pipe_proc_tests/ext.py
@@ -1,6 +1,8 @@
 #! /usr/bin/env python
 """ Create files for ext unit test """
 
+from subprocess import check_output
+
 import nmrglue.fileio.pipe as pipe
 import nmrglue.process.pipe_proc as p
 
@@ -31,3 +33,37 @@
 d, a = pipe.read("time_complex.fid")
 d, a = p.ext(d, a, x1=5, xn=200, round=10)
 pipe.write("ext7.glue", d, a, overwrite=True)
+
+
+pipe_command = """\
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT  -auto \
+-ov -out time-freq.c.ft1"""
+check_output(pipe_command, shell=True)
+
+d, a = pipe.read("time-freq.c.ft1")
+d, a = p.ext(d, a, left=True, sw=True)
+pipe.write("ext8.glue", d, a, overwrite=True)
+
+d, a = pipe.read("time-freq.c.ft1")
+d, a = p.ext(d, a, right=True, sw=True)
+pipe.write("ext9.glue", d, a, overwrite=True)
+
+os.remove("time-freq.c.ft1")
+
+
+pipe_command = """\
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT  -auto -di \
+-ov -out time-freq.r.ft1"""
+check_output(pipe_command, shell=True)
+
+d, a = pipe.read("time-freq.r.ft1")
+d, a = p.ext(d, a, left=True, sw=True)
+pipe.write("ext10.glue", d, a, overwrite=True)
+
+d, a = pipe.read("time-freq.r.ft1")
+d, a = p.ext(d, a, right=True, sw=True)
+pipe.write("ext11.glue", d, a, overwrite=True)
+
+os.remove("time-freq.r.ft1")
diff --git a/tests/pipe_proc_tests/tp.com b/tests/pipe_proc_tests/tp.com
@@ -11,3 +11,32 @@ nmrPipe -in ./time_complex.fid                \
 nmrPipe -in ./time_complex.fid                \
 | nmrPipe  -fn TP  -nohyper \
 -ov -out tp3.dat
+
+
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT -auto \
+-ov -out time-freq.c.ft1
+
+nmrPipe -in ./time-freq.c.ft1                \
+| nmrPipe  -fn TP -hyper\
+-ov -out tp4.dat
+
+nmrPipe -in ./time-freq.c.ft1                \
+| nmrPipe  -fn TP -auto\
+-ov -out tp5.dat
+
+rm -f time-freq.c.ft1
+
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT -auto -di \
+-ov -out time-freq.r.ft1
+
+nmrPipe -in ./time-freq.r.ft1                \
+| nmrPipe -fn TP \
+-ov -out tp6.dat
+
+nmrPipe -in ./time-freq.r.ft1                \
+| nmrPipe  -fn TP -auto \
+-ov -out tp7.dat
+
+rm -f time-freq.r.ft1
diff --git a/tests/pipe_proc_tests/tp.py b/tests/pipe_proc_tests/tp.py
@@ -1,6 +1,8 @@
 #! /usr/bin/env python
 """ Create files for tp unit test """
 
+from subprocess import check_output
+
 import nmrglue.fileio.pipe as pipe
 import nmrglue.process.pipe_proc as p
 
@@ -15,3 +17,36 @@
 d, a = pipe.read("time_complex.fid")
 d, a = p.tp(d, a, nohyper=True)
 pipe.write("tp3.glue", d, a, overwrite=True)
+
+
+pipe_command = """\
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT  -auto \
+-ov -out time-freq.c.ft1"""
+check_output(pipe_command, shell=True)
+
+d, a = pipe.read("time-freq.c.ft1")
+d, a = p.tp(d, a, hyper=True)
+pipe.write("tp4.glue", d, a, overwrite=True)
+
+d, a = pipe.read("time-freq.c.ft1")
+d, a = p.tp(d, a, auto=True)
+pipe.write("tp5.glue", d, a, overwrite=True)
+
+os.remove("time-freq.c.ft1")
+
+pipe_command = """\
+nmrPipe -in ./time_complex.fid                \
+| nmrPipe  -fn FT  -auto -di \
+-ov -out time-freq.r.ft1"""
+check_output(pipe_command, shell=True)
+
+d, a = pipe.read("time-freq.r.ft1")
+d, a = p.tp(d, a)
+pipe.write("tp6.glue", d, a, overwrite=True)
+
+d, a = pipe.read("time-freq.r.ft1")
+d, a = p.tp(d, a, auto=True)
+pipe.write("tp7.glue", d, a, overwrite=True)
+
+os.remove("time-freq.r.ft1")
diff --git a/tests/test_pipe_proc.py b/tests/test_pipe_proc.py
@@ -6,7 +6,8 @@
 
 # Framework functions
 
-def _perform_test(glue_script, pipe_script, glue_files, pipe_files):
+def _perform_test(glue_script, pipe_script, glue_files, pipe_files, 
+                  ignore_pipe_display=False):
     """ 
     """
     cwd_backup = os.getcwd()    # save the current working directory
@@ -26,7 +27,8 @@ def _perform_test(glue_script, pipe_script, glue_files, pipe_files):
         os.remove(glue_file)
         os.remove(pipe_file)
         r1, r2 = ng.misc.pair_similar(glue_dic, glue_data, pipe_dic,
-                                        pipe_data, True)
+                                        pipe_data, True, 
+                                        ignore_pipe_display=ignore_pipe_display)
         print glue_file, pipe_file, r1, r2
         assert r1 is True
         assert r2 is True
@@ -43,8 +45,9 @@ def _standard_args(func_name, num_files):
     glue_script = './' + func_name + '.py'
     return glue_script, pipe_script, glue_files, pipe_files
 
-def _standard_test(func_name, num_files):
-    return _perform_test(*_standard_args(func_name, num_files))
+def _standard_test(func_name, num_files, ignore_pipe_display=False):
+    return _perform_test(*_standard_args(func_name, num_files), 
+                         ignore_pipe_display =ignore_pipe_display)
 
 
 #########################
@@ -153,7 +156,7 @@ def test_ps():
 
 def test_tp():
     """ TP function """
-    return _standard_test('tp', 3)
+    return _standard_test('tp', 7, ignore_pipe_display=True)
 
 def test_ytp():
     """ YTP function """
@@ -181,7 +184,7 @@ def test_dx():
 
 def test_ext():
     """ EXT function """
-    return _standard_test('ext', 7)
+    return _standard_test('ext', 11, ignore_pipe_display=True)
 
 def test_integ():
     """ INTEG function """
