Splitting reading and interpolating into 2 functions

Change-Id: I02ada28a6a04cc6dd91dae1e560eb72ceb3f8987

brukeropusreader/opus_data.py

@@ -2,12 +2,17 @@ import matplotlib.pyplot as plt
 import csv
 import numpy as np
 from numpy import linalg
+from scipy.interpolate import interp1d
 
 
 class NoInterpolatedDataException(Exception):
     pass
 
 
+class WrongWavelengthsInConf(Exception):
+    pass
+
+
 class OpusData(object):
     def __init__(self, raw_data, interp=None, meta=None):
         self.raw_data = raw_data
@@ -46,3 +51,39 @@ class OpusData(object):
                      self.interpolated_data[1],
                      'ro')
             plt.show()
+
+    def gen_interp_waves(self, conf):
+        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)):
+            a -= wunit
+            iwavenumber[i] = a
+        return iwavenumber
+
+    def interpolate_spectra(self, conf):
+        xav, yav = self.raw_data[0], self.raw_data[1]
+        ab_wavenumbers = self.raw_data[0]
+        iwavenumber = self.gen_interp_waves(conf)
+
+        xa_min = min(ab_wavenumbers)
+        xa_max = max(ab_wavenumbers)
+        n_interp = conf.iwsize
+        yi = []
+
+        f2 = interp1d(xav, yav, kind='cubic', assume_sorted=True)
+
+        for k in range(n_interp):
+            if iwavenumber[k] < xa_min:
+                if k == n_interp - 1:
+                    yi.append(yav[0])
+                else:
+                    print("Wrong wavelenghts for interpolating data")
+            elif iwavenumber[k] > xa_max:
+                if k == 0:
+                    yi.append(yav[-1])
+                else:
+                    raise WrongWavelengthsInConf()
+            else:
+                yi.append(f2(iwavenumber[k]))
+        return iwavenumber, yi

brukeropusreader/opus_reader.py

@@ -1,8 +1,7 @@
 import numpy as np
 from struct import unpack_from
-from scipy.interpolate import interp1d
+from .utils import find_all
-from utils import find_all
+from .opus_data import OpusData
-from opus_data import OpusData
 from itertools import product
 
 
@@ -10,11 +9,7 @@ class NoAbsorbanceSpectra(Exception):
     pass
 
 
-class WrongWavelengthsInConf(Exception):
+def opus_reader(filepath):
-    pass
-
-
-def opus_reader(filepath, conf, interpolate=True):
     with open(filepath, 'rb') as f:
         buff = f.read()
 
@@ -23,19 +18,11 @@ def opus_reader(filepath, conf, interpolate=True):
     # Choose best ab spectra
     ab_spectra, ab_wavenumbers = choose_ab(fxv_spc, spc, wavenumbers)
 
-    pairs = reversed(zip(ab_wavenumbers, ab_spectra))
+    wave_num_abs_pair = reversed(zip(ab_wavenumbers, ab_spectra))
 
-    # AB spectra and wave extracted, now interpolating
-    if interpolate:
-        iwavenumber, yi = interpolate_spectra(pairs, ab_wavenumbers, conf)
-
-    # Spectra succesfully interpolated, now extracting metadata
     meta = get_meta_data(buff)
 
-    if interpolate:
+    return OpusData(zip(*wave_num_abs_pair), meta=meta)
-        return OpusData(zip(*pairs), interp=(iwavenumber, yi), meta=meta)
-    else:
-        return OpusData(zip(*pairs), meta=meta)
 
 
 def choose_ab(fxv_spc, spc, wavenumbers):
@@ -123,44 +110,6 @@ def generate_wavelengths(lxv_spc, fxv_spc, npt_spc):
     return wavenumbers
 
 
-def generate_interpolated_wavenumbers(conf):
-    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)):
-        a -= wunit
-        iwavenumber[i] = a
-    return iwavenumber
-
-
-def interpolate_spectra(pairs, ab_wavenumbers, conf):
-    iwavenumber = generate_interpolated_wavenumbers(conf)
-
-    xav, yav = zip(*pairs)[0], zip(*pairs)[1]
-
-    xa_min = min(ab_wavenumbers)
-    xa_max = max(ab_wavenumbers)
-    n_interp = conf.iwsize
-    yi = []
-
-    f2 = interp1d(xav, yav, kind='cubic', assume_sorted=True)
-
-    for k in range(n_interp):
-        if iwavenumber[k] < xa_min:
-            if k == n_interp - 1:
-                yi.append(yav[0])
-            else:
-                print("Wrong wavelenghts for interpolating data")
-        elif iwavenumber[k] > xa_max:
-            if k == 0:
-                yi.append(yav[-1])
-            else:
-                raise WrongWavelengthsInConf()
-        else:
-            yi.append(f2(iwavenumber[k]))
-    return iwavenumber, yi
-
-
 def get_meta_data(buff):
     # Getting source of instruments
     all_ins = tuple(find_all('INS', buff))

example.py

@@ -0,0 +1,26 @@
+from brukeropusreader.opus_reader import opus_reader
+from os import walk
+import os
+import sys
+
+
+def filter_fun(nm):
+    return (nm[0] != '.') and (nm[-2:] in ('.0', '.1', '.2', '.3'))
+
+
+def main(path_to_opus_files):
+    i = 0
+    all_files = 0
+    for path, subdirs, files in walk(path_to_opus_files):
+        for name in filter(filter_fun, files):
+            all_files += 1
+            try:
+                od = opus_reader(os.path.join(path, name))
+                od.plot_raw()
+            except Exception as e:
+                i += 1
+                print i, ":", name, str(e)
+
+
+if __name__ == '__main__':
+    main(sys.argv[1])

get_bart_result.R

@@ -1,6 +0,0 @@
-library(rbart)
-
-save.soil <- function(opus.file.path, conf.path, output.file='result.csv', output.path='./'){
-  df = read.opus(opus.file.path, conf.path)
-  write.csv(df, paste(output.path, output.file, sep=""))
-}

requirements.in

@@ -0,0 +1,3 @@
+numpy
+scipy
+matplotlib

requirements.txt

@@ -1,2 +1,16 @@
-numpy
+#
-scipy
+# This file is autogenerated by pip-compile
+# To update, run:
+#
+#    pip-compile --output-file requirements.txt requirements.in
+#
+backports.functools-lru-cache==1.4  # via matplotlib
+cycler==0.10.0            # via matplotlib
+matplotlib==2.1.0
+numpy==1.13.3
+pyparsing==2.2.0          # via matplotlib
+python-dateutil==2.6.1    # via matplotlib
+pytz==2017.2              # via matplotlib
+scipy==0.19.1
+six==1.11.0               # via cycler, matplotlib, python-dateutil
+subprocess32==3.2.7       # via matplotlib

setup.py

@@ -0,0 +1,10 @@
+from distutils.core import setup
+
+
+setup(name='bruker-opus-reader',
+      version='1.0',
+      description='Bruker OPUS files reader',
+      author='t2',
+      author_email='t2@qed.ai',
+      packages=['brukeropusreader'],
+      )