Merge "Moving bruker opus reader to python 3"

.gitignore

@@ -1,2 +1,2 @@
 *.pyc
-*.csv
+*.csv

brukeropusreader/opus_data.py

@@ -44,8 +44,8 @@ class OpusData(object):
             csv_reader = csv.reader(csv_file)
             x_r = np.array(map(lambda x: float(x[1:]), next(csv_reader)[2:]))
             y_r = np.array(map(lambda x: float(x), next(csv_reader)[2:]))
-            dist = linalg.norm(y_r-self.interpolated_data[1], ord=1)
-            print "L1 distance between rbart and python versions:", dist
+            dist = linalg.norm(y_r - self.interpolated_data[1], ord=1)
+            print("L1 distance between rbart and python versions:", dist)
             plt.plot(x_r, y_r, 'bo')
             plt.plot(self.interpolated_data[0],
                      self.interpolated_data[1],
@@ -56,7 +56,7 @@ class OpusData(object):
         wunit = (conf.wave_start - conf.wave_end) / (float(conf.iwsize - 1))
         a = conf.wave_start + wunit
         iwavenumber = [0] * conf.iwsize
-        for i in xrange(len(iwavenumber)):
+        for i in range(len(iwavenumber)):
             a -= wunit
             iwavenumber[i] = a
         return iwavenumber

brukeropusreader/opus_reader.py

@@ -18,11 +18,11 @@ def opus_reader(filepath):
     # Choose best ab spectra
     ab_spectra, ab_wavenumbers = choose_ab(fxv_spc, spc, wavenumbers)
 
-    wave_num_abs_pair = reversed(zip(ab_wavenumbers, ab_spectra))
+    wave_num_abs_pair = reversed(list(zip(ab_wavenumbers, ab_spectra)))
 
     meta = get_metadata(buff)
 
-    return OpusData(zip(*wave_num_abs_pair), meta=meta)
+    return OpusData(list(zip(*wave_num_abs_pair)), meta=meta)
 
 
 def choose_ab(fxv_spc, spc, wavenumbers):
@@ -37,7 +37,7 @@ def choose_ab(fxv_spc, spc, wavenumbers):
         if np.average(spc[x]) > 0.25:
             ab.append(x)
     if len(ab) > 1:
-        spc_avg = map(lambda x: np.average(spc[x]), ab)
+        spc_avg = [np.average(spc[x]) for x in ab]
         max_avg_index = spc_avg.index(max(spc_avg))
         ab_p = ab[max_avg_index]
     elif len(ab) == 1:
@@ -51,19 +51,19 @@ def choose_ab(fxv_spc, spc, wavenumbers):
 
 
 def keyword_positions(buff):
-    end = np.array(list(find_all("END", buff))) + 12
-    npt_all = np.array(list(find_all("NPT", buff))) + 8
-    fxv_all = np.array(list(find_all("FXV", buff))) + 8
-    lxv_all = np.array(list(find_all("LXV", buff))) + 8
+    end = np.array(list(find_all(b'END', buff))) + 12
+    npt_all = np.array(list(find_all(b'NPT', buff))) + 8
+    fxv_all = np.array(list(find_all(b'FXV', buff))) + 8
+    lxv_all = np.array(list(find_all(b'LXV', buff))) + 8
     return end, npt_all, fxv_all, lxv_all
 
 
 def filter_unpaired(fxv_all, lxv_all):
     if len(fxv_all) != len(lxv_all):
         prod = product(fxv_all, lxv_all)
-        correct_adressess = zip(*filter(lambda d: (d[1] - d[0]) == 16, prod))
-        fxv_all = np.array(correct_adressess[0])
-        lxv_all = np.array(correct_adressess[1])
+        corr_adr = list(zip(*filter(lambda d: (d[1] - d[0]) == 16, prod)))
+        fxv_all = np.array(corr_adr[0])
+        lxv_all = np.array(corr_adr[1])
     return fxv_all, lxv_all
 
 
@@ -72,15 +72,15 @@ def read_all_spectras(buff):
     fxv_all, lxv_all = filter_unpaired(fxv_all, lxv_all)
 
     # Number of wavepoints
-    npt = [unpack_from("<i", buff, adr)[0] for adr in npt_all]
-    # "end_spc is vector of offsets where spectra start"
+    npt = [unpack_from('<i', buff, adr)[0] for adr in npt_all]
+    # 'end_spc is vector of offsets where spectra start'
     end_spc = end[np.where(np.diff(end) > 4 * min(npt))]
     spc_param_list = {'npt': npt_all, 'fxv': fxv_all, 'lxv': lxv_all}
 
     # Filtering some corrupted series
     param_spc = filter_spc_params(end_spc, spc_param_list, npt_all)
     # Number of points in correct spectras
-    npt_spc = [unpack_from("<i", buff, adr)[0] for adr in param_spc["npt"]]
+    npt_spc = [unpack_from('<i', buff, adr)[0] for adr in param_spc['npt']]
     npt_spc = np.array(npt_spc)
 
     mask = npt_spc > 0
@@ -89,14 +89,14 @@ def read_all_spectras(buff):
     npt_spc = npt_spc[mask]
 
     def read_spec(x):
-        return np.array(unpack_from("<" + str(x[1]) + "f", buff, x[0] - 4))
+        return np.array(unpack_from('<' + str(x[1]) + 'f', buff, x[0] - 4))
 
     def read_waves(x):
-        return unpack_from("<2d", buff, x)[0]
+        return unpack_from('<2d', buff, x)[0]
 
-    spc = map(read_spec, zip(param_spc['end'], npt_spc))
-    fxv_spc = np.array(map(read_waves, param_spc["fxv"]))
-    lxv_spc = map(lambda x: unpack_from("<2d", buff, x)[0], param_spc["lxv"])
+    spc = list(map(read_spec, zip(param_spc['end'], npt_spc)))
+    fxv_spc = np.array([read_waves(x) for x in param_spc['fxv']])
+    lxv_spc = [unpack_from('<2d', buff, x)[0] for x in param_spc['lxv']]
     wavenumbers = generate_wavelengths(lxv_spc, fxv_spc, npt_spc)
 
     return fxv_spc, spc, wavenumbers
@@ -113,17 +113,17 @@ def generate_wavelengths(lxv_spc, fxv_spc, npt_spc):
 
 def get_metadata(buff):
     # Getting source of instruments
-    all_ins = tuple(find_all('INS', buff))
-    inst = unpack_from("<3s", buff, all_ins[-1] + 8)[0]
+    all_ins = tuple(find_all(b'INS', buff))
+    inst = unpack_from('<3s', buff, all_ins[-1] + 8)[0]
     # Getting source of infrared <NIR/MIR>
-    all_src = tuple(find_all('SRC', buff))
-    src = unpack_from("<3s", buff, all_src[-1] + 5)[0]
+    all_src = tuple(find_all(b'SRC', buff))
+    src = unpack_from('<3s', buff, all_src[-1] + 5)[0]
 
-    dat = buff.find('DAT') + 8
-    scandate = unpack_from("10s", buff, dat)[0]
+    dat = buff.find(b'DAT') + 8
+    scandate = unpack_from('10s', buff, dat)[0]
 
-    snm = buff.find('SNM') + 8
-    snm_lab_material = unpack_from("22s", buff, snm)[0]
+    snm = buff.find(b'SNM') + 8
+    snm_lab_material = unpack_from('22s', buff, snm)[0]
 
     meta = {'ins': inst,
             'src': src,

example.py

@@ -19,7 +19,7 @@ def main(path_to_opus_files):
                 od.plot_raw()
             except Exception as e:
                 i += 1
-                print i, ":", name, str(e)
+                print(i, ":", name, str(e))
 
 
 if __name__ == '__main__':