STY: PEP8 on all files

nmrglue/analysis/linesh.py

@@ -134,7 +134,7 @@ def estimate_scales(spectrum, centers, box_width, scale_axis=0):
     # loop over the box centers
     for bc in bcenters:
 
-    # calculate box limits
+        # calculate box limits
         bmin = [max(c - w, 0) for c, w in zip(bc, box_width)]
         bmax = [min(c + w + 1, s) for c, w, s in zip(bc, box_width, shape)]
 
@@ -502,16 +502,16 @@ def fit_NDregion(region, lineshapes, params, amps, bounds=None,
         raise ValueError(err)
 
     # DEBUGGING
-    #print("--------------------------------")
-    #print(region)
-    #print(ls_classes)
-    #print(p0)
-    #print(p_bounds)
-    #print(n_peaks)
-    #print(dim_nparam)
-    #print("=================================")
-    #for i,j in zip(p0,p_bounds):
-    #    print(i, j)
+    # print("--------------------------------")
+    # print(region)
+    # print(ls_classes)
+    # print(p0)
+    # print(p_bounds)
+    # print(n_peaks)
+    # print(dim_nparam)
+    # print("=================================")
+    # for i,j in zip(p0,p_bounds):
+    #     print(i, j)
 
     # include full_output=True when errors requested
     if error_flag:
@@ -521,7 +521,7 @@ def fit_NDregion(region, lineshapes, params, amps, bounds=None,
     r = f_NDregion(region, ls_classes, p0, p_bounds, n_peaks, wmask, **kw)
 
     # DEBUGGING
-    #print(r)
+    # print(r)
 
     # unpack results depending of if full output requested
     if "full_output" in kw and kw["full_output"]:
@@ -622,10 +622,10 @@ def sim_NDregion(shape, lineshapes, params, amps):
     p = list(amps) + p   # amplitudes appended to front of p
 
     # DEBUGGING
-    #print("p",p)
-    #print("shape",shape)
-    #print("ls_classes",ls_classes)
-    #print("n_peaks",n_peaks)
+    # print("p",p)
+    # print("shape",shape)
+    # print("ls_classes",ls_classes)
+    # print("n_peaks",n_peaks)
 
     return s_NDregion(p, shape, ls_classes, n_peaks)
 
@@ -757,10 +757,10 @@ def s_single_NDregion(p, shape, ls_classes):
     r = np.array(A, dtype='float')
 
     for length, ls_class in zip(shape, ls_classes):
-        #print("Making lineshape of", ls_class.name, "with length:", length)
+        # print("Making lineshape of", ls_class.name, "with length:", length)
         s_p = [p.pop(0) for i in range(ls_class.nparam(length))]
         ls = ls_class.sim(length, s_p)
-        #print("Lineshape is:", ls)
+        # print("Lineshape is:", ls)
         r = np.kron(r, ls)   # vector direct product flattened
     return r.reshape(shape)
 

nmrglue/analysis/peakpick.py

@@ -207,8 +207,8 @@ def pick(data, pthres, nthres=None, msep=None, algorithm='connected',
     seg_slices = pseg + nseg
     scales = [[]] * len(locations)
     amps = [[]] * len(locations)
-    #scales = np.zeros(np.array(locations).shape,dtype=float)
-    #amps = np.zeros(len(locations),dtype=float)
+    # scales = np.zeros(np.array(locations).shape,dtype=float)
+    # amps = np.zeros(len(locations),dtype=float)
 
     for i, (l, seg_slice) in enumerate(zip(locations, seg_slices)):
         null, scales[i], amps[i] = guess_params_slice(data, l, seg_slice,

nmrglue/fileio/__init__.py

@@ -1,6 +1,6 @@
 from . import bruker
 from . import convert
-#from . import glue
+# from . import glue
 from . import pipe
 from . import rnmrtk
 from . import simpson

nmrglue/fileio/bruker.py

@@ -1473,7 +1473,7 @@ def rm_dig_filter(data, decim, dspfvs, grpdly=0):
     add = int(max(skip - 6, 0))           # 6 less, or 0
 
     # DEBUG
-    #print("phase: %f, skip: %i add: %i"%(phase,skip,add))
+    # print("phase: %f, skip: %i add: %i"%(phase,skip,add))
 
     # frequency shift
     pdata = proc_base.fsh2(data, phase)
@@ -1524,7 +1524,7 @@ def read_jcamp(filename):
             break
 
         if line[:6] == "##END=":
-            #print("End of file")
+            # print("End of file")
             break
         elif line[:2] == "$$":
             dic["_comments"].append(line)
@@ -1797,7 +1797,7 @@ def read_pprog(filename):
 
         # skip blank lines and include lines
         if text == "" or text[0] == "#":
-            #print(line,"--Blank, Comment or Include")
+            # print(line,"--Blank, Comment or Include")
             continue
 
         # see if we have quotes and have an assigment
@@ -1811,13 +1811,13 @@ def read_pprog(filename):
                 if len(t) >= 2:
                     key, value = t[0], t[1]
                     var[key] = value
-                    #print(line,"--Assignment")
+                    # print(line,"--Assignment")
                 else:
                     pass
-                    #print(line,"--Statement")
+                    # print(line,"--Statement")
                 continue
             else:
-                #print(line,"--Statement")
+                # print(line,"--Statement")
                 continue
 
         # loops begin with lo
@@ -1828,7 +1828,7 @@ def read_pprog(filename):
             incr.append([])
             phase.append([])
             ph_extra.append([])
-            #print(line,"--Loop")
+            # print(line,"--Loop")
             continue
 
         tokens = text.split()
@@ -1839,12 +1839,12 @@ def read_pprog(filename):
             # store N to incr list
             if token2.startswith('id') or token2.startswith('dd'):
                 incr[len(loop)].append(int(token2[2:]))
-                #print(line,"--Increment")
+                # print(line,"--Increment")
                 continue
 
             if token2.startswith("ipu") or token2.startswith("dpu"):
                 incr[len(loop)].append(int(token2[3:]))
-                #print(line,"--Increment")
+                # print(line,"--Increment")
                 continue
 
             # phase statement have ip or dp
@@ -1859,10 +1859,10 @@ def read_pprog(filename):
                     ph_extra[len(loop)].append("")
                 else:
                     ph_extra[len(loop)].append(text[last:].strip())
-                #print(line,"--Phase")
+                # print(line,"--Phase")
                 continue
 
-            #print(line,"--Unimportant")
+            # print(line,"--Unimportant")
 
     f.close()
 

nmrglue/fileio/convert.py

@@ -88,7 +88,7 @@ def __procdata(self):
         # processing for input type
         # sign alt. indirect dimension
         if data.ndim >= 2 and "alt_id_sign" in self._iproc:
-            #data[1::2] = -data[1::2]
+            # data[1::2] = -data[1::2]
             s = [slice(None, None, None)] * data.ndim
             for i in range(data.ndim - 1):
                 s[i] = slice(1, None, 2)

nmrglue/fileio/fileiobase.py

@@ -27,10 +27,10 @@ def create_blank_udic(ndim):
         d["complex"] = True     # Quadrature, True when dimension is complex
         d["obs"] = 999.99       # Observation frequency in MHz
         d["car"] = 999.99       # Carrier frequency in Hz
-        d["size"] = 1           # Number of points in dimension based on the
-                                # shape of the data array. As such the direct
-                                # dimension (-1) size is R|I, all indirect
-                                # dimensions are R+I
+        # Number of points in dimension based on the shape of the data array.
+        # As such the direct dimension (-1) size is R|I, all indirect
+        # dimensions are R+I
+        d["size"] = 1
 
         d["label"] = ["X", "Y", "Z", "A"][i]    # name of dimension
 
@@ -141,18 +141,18 @@ def __unit2pnt(self, val, units):
             pts = self.__us2pts(val)
         else:
             raise ValueError("invalid unit type")
-        #if self._cplx:
-        #    return pts+round(pts)
-        #else:
+        # if self._cplx:
+        #     return pts+round(pts)
+        # else:
         return pts
 
     def __pnt2unit(self, val, units):
         """
         Convert points to units
         """
         units = units.upper()
-        #if self._cplx:
-        #    val = val-round(val)
+        # if self._cplx:
+        #     val = val-round(val)
         if units == "PPM":
             k = self.__pts2ppm(val)
         elif units == "HZ":

nmrglue/fileio/pipe.py

@@ -79,7 +79,7 @@ def read_table(filename):
     dtd['formats'] = [p2f[i[-1]] for i in pformat]
 
     # DEBUG
-    #print(dtd['names'],dtd['formats'])
+    # print(dtd['names'],dtd['formats'])
     s = StringIO("".join(dl))
 
     rec = np.recfromtxt(s, dtype=dtd, comments='XXXXXXXXXXX')
@@ -371,12 +371,12 @@ def add_axis_to_dic(dic, adic, n):
 
     # origin (last point) is CAR*OBS-SW*(N/2-1)/N
     # see Fig 3.1 on p.36 of Hoch and Stern
-    #print("fn:",n)
-    #print("CAR:",dic[fn+"CAR"])
-    #print("OBS:",dic[fn+"OBS"])
-    #print("SW:",dic[fn+"SW"])
-    #print("osize:",osize)
-    #print("CENTER:",dic[fn+"CENTER"])
+    # print("fn:",n)
+    # print("CAR:",dic[fn+"CAR"])
+    # print("OBS:",dic[fn+"OBS"])
+    # print("SW:",dic[fn+"SW"])
+    # print("osize:",osize)
+    # print("CENTER:",dic[fn+"CENTER"])
     dic[fn + "ORIG"] = (dic[fn + "CAR"] * dic[fn + "OBS"] - dic[fn + "SW"] *
                         (osize - dic[fn + "CENTER"]) / osize)
 
@@ -1049,7 +1049,7 @@ def put_data(filename, fdata, data, overwrite=False):
     Put fdata and data to 2D NMRPipe.
     """
     if data.dtype != 'float32':
-        #print(data.dtype)
+        # print(data.dtype)
         raise TypeError('data.dtype is not float32')
     if fdata.dtype != 'float32':
         raise TypeError('fdata.dtype is not float32')
@@ -1106,7 +1106,7 @@ def write_slice_3D(filemask, dic, data, shape, slices):
     # loop over the requested z-slice
     for i, f in enumerate(fnames[sz]):
 
-        #print("i:",i,"f:",f)
+        # print("i:",i,"f:",f)
         if os.path.isfile(f) is False:
             # file doesn't exist, create a empty one
             ndata = np.zeros((dy, dx), dtype=data.dtype)
@@ -1331,7 +1331,7 @@ def __init__(self, filemask, in_lead="x", out_lead="DEFAULT"):
         elif self.in_lead == "z":
             # transpose to Y(XZ)
             self.idic, self.pipe_3d = transpose_3D(self.dic, self.pipe_3d,
-                                                  (1, 2, 0))
+                                                   (1, 2, 0))
             fn = "FDF" + str(int(self.idic["FDDIMORDER1"]))
             if self.idic[fn + "QUADFLAG"] != 1.0:   # z axis is complex
                 self.needs_pack_complex = True
@@ -1408,11 +1408,11 @@ def write(self, filemask, plane, dic):
             raise ValueError("invalid in_lead")  # this should never be raised
 
         # DEBUGGING
-        #print("Writing out slice :",self.i)
-        #print("shape:",shape)
-        #print("plane.shape",plane.shape)
-        #print("sx,sy,sz",sx,sy,sz)
-        #print(dic["FDFILECOUNT"])
+        # print("Writing out slice :",self.i)
+        # print("shape:",shape)
+        # print("plane.shape",plane.shape)
+        # print("sx,sy,sz",sx,sy,sz)
+        # print(dic["FDFILECOUNT"])
         write_slice_3D(filemask, dic, plane, shape, (sz, sy, sx))
 
 #####################

nmrglue/fileio/rnmrtk.py

@@ -524,12 +524,12 @@ def interleave_data(data):
     Interleave real, imag data in data
     """
     return data.view('float32')
-    #size = list(data.shape)
-    #size[-1] = size[-1]*2
-    #data_out = np.empty(size,dtype="float32")
-    #data_out[...,::2] = data.real
-    #data_out[...,1::2] = data.imag
-    #return data_out
+    # size = list(data.shape)
+    # size[-1] = size[-1]*2
+    # data_out = np.empty(size,dtype="float32")
+    # data_out[...,::2] = data.real
+    # data_out[...,1::2] = data.imag
+    # return data_out
 
 ######################
 # low-memory objects #

nmrglue/fileio/simpson.py

@@ -161,7 +161,7 @@ def read_text(filename):
             dic[key] = int(dic[key])
 
     # DEBUGGING
-    #return dic
+    # return dic
 
     if "NI" in dic:     # 2D data
         data = np.empty((dic['NI'], dic['NP']), dtype='complex64')
@@ -328,7 +328,7 @@ def read_binary(filename):
             dic[key] = int(dic[key])
 
     # DEBUGGING
-    #return dic, f
+    # return dic, f
 
     # extract characters from data block
     chardata = "".join([line.strip('\n') for line in f])
@@ -343,7 +343,7 @@ def read_binary(filename):
         bytes += chars2bytes(chardata[i * 4:(i + 1) * 4])
 
     # DEBUGGING
-    #return dic, bytes
+    # return dic, bytes
     # convert every 4 'bytes' to a float, then complex data
     num_points, _num_pad = divmod(len(bytes), 4)
     data = np.empty((num_points, ), dtype='float32')