Minor changes

- Fixed par1-error when selecting None
- Fixed par1/2-error when selecting data blocks with longer data name
- Minor changes to color/font-size

Author: pyahmed

README.rst

@@ -1,34 +1,42 @@
+======
 PyCORN
 ======
 
 A script to extract data from UNICORN result (.res) files and plot them.
 
 .. image:: https://raw.githubusercontent.com/pyahmed/PyCORN/master/samples/sample1_2009Jun16no001_plot.jpg
 
+A script extract data from .res (results) files generated by UNICORN Chromatography software supplied with AKTA Systems. This script will find all data blocks, extract the data and write out csv-files. If you have matplotlib installed it will also plot all the curves including fractions if present. Plots can be saved in any format supported by matplotlib (default is pdf). Alternatively you may import pycorn into your script and access the data inside res-files.
+
+----
 
-A script to extract data from .res (results) files generated by UNICORN Chromatography software supplied with AKTA Systems. This script will
-find all data blocks, extract the data and write out csv-files. If you have matplotlib installed it will also plot all the curves including
-fractions if present. Plots can be saved in any format supported by matplotlib (default is pdf). Alternatively you may import pycorn into your script and access the data inside res-files.
+News
+----
+- v0.13 released, available on PyPI, see docs/CHANGES.txt
 
-Installation:
 
+Installation
+------------
 - pip install pycorn
 
-Limitations:
 
+Limitations
+-----------
 - See https://github.com/pyahmed/PyCORN/issues
 
-Requirements:
 
-- Python 2.7 or 3.x (Tested on Windows 7 / Mac OSX) 
-- optional: working matplotlib installation (for plotting)
+Requirements
+------------
+- Python 2.7 or 3.x (Tested on Linux / Windows 7 / Mac OSX) 
+- optional: matplotlib (for plotting)
 
-Usage:
 
+Usage
+-----
 - See docs/USAGE_pycorn-bin.txt if you want to extract/plot data directly
-- See docs/USAGE_pycorn_module.txt if you want to use it as module
-
+- See docs/USAGE_pycorn_module.txt if you want to import it into your script
 
-License:
 
+License
+-------
 - GPLv2 see docs/LICENSE.txt

examplescripts/pycorn-bin.py

@@ -48,7 +48,7 @@
                     help="Upper bound on the x-axis",
                     metavar="#")
 group1.add_argument("--par1", type = str, default='Cond',
-                    help="Data for 2nd y-axis (Default=Cond)")
+                    help="Data for 2nd y-axis (Default=Cond), to disable 2nd y-axis, use --par1 None")
 group1.add_argument("--par2", type = str, default=None,
                     help="Data for 3rd y-axis (Default=None)")                 
 group1.add_argument('-f', '--format', type = str,
@@ -126,7 +126,6 @@ def smartscale(inp):
         KeyError
         uv2_data = None
         uv3_data = None
-    frac_delta = []
     try:
         frac_data = inp['Fractions']['data']
         frac_x, frac_y = xy_data(frac_data)
@@ -187,33 +186,43 @@ def plotterX(inp,fname):
             p0, = host.plot(x_dat, y_dat, label=inp[i]['data_name'], color=stl['color'],
                             ls=stl['ls'], lw=stl['lw'],alpha=stl['alpha'])
     if args.par1:
-        par1_inp = args.par1
-        par1 = host.twinx()
-        par1_data = inp[par1_inp]
-        stl = styles[par1_inp]
-        par1.set_ylabel(par1_data['data_name'] + " (" + par1_data['unit'] + ")", color=stl['color'])
-        x_dat_p1, y_dat_p1 = xy_data(par1_data['data'])
-        p1_ymin, p1_ymax = expander(min(y_dat_p1), max(y_dat_p1), 0.085)
-        par1.set_ylim(p1_ymin, p1_ymax)
-        print("Plotting: " + par1_data['data_name'])
-        p1, = par1.plot(x_dat_p1, y_dat_p1, label=par1_data['data_name'], color=stl['color'],
-                        ls=stl['ls'], lw=stl['lw'], alpha=stl['alpha'])
+        try:
+            par1_inp = args.par1
+            par1 = host.twinx()
+            par1_data = inp[par1_inp]
+            stl = styles[par1_inp[:4]]
+            par1.set_ylabel(par1_data['data_name'] + " (" + par1_data['unit'] + ")", color=stl['color'])
+            x_dat_p1, y_dat_p1 = xy_data(par1_data['data'])
+            p1_ymin, p1_ymax = expander(min(y_dat_p1), max(y_dat_p1), 0.085)
+            par1.set_ylim(p1_ymin, p1_ymax)
+            print("Plotting: " + par1_data['data_name'])
+            p1, = par1.plot(x_dat_p1, y_dat_p1, label=par1_data['data_name'], 
+            color=stl['color'], ls=stl['ls'], lw=stl['lw'], alpha=stl['alpha'])
+        except:
+            KeyError
+            if par1_inp != None:
+                print("Warning: Data block chosen for par1 does not exist!")
     if args.par2:
-        par2_inp = args.par2
-        par2 = host.twinx()
-        offset = 60
-        new_fixed_axis = par2.get_grid_helper().new_fixed_axis
-        par2.axis["right"] = new_fixed_axis(loc="right", axes=par2, offset=(offset, 0))  
-        par2.axis["right"].toggle(all=True)
-        par2_data = inp[par2_inp]
-        stl = styles[par2_inp]
-        par2.set_ylabel(par2_data['data_name'] + " (" + par2_data['unit'] + ")", color=stl['color'])
-        x_dat_p2, y_dat_p2 = xy_data(par2_data['data'])
-        p2_ymin, p2_ymax = expander(min(y_dat_p2), max(y_dat_p2), 0.075)
-        par2.set_ylim(p2_ymin, p2_ymax)
-        print("Plotting: " + par2_data['data_name'])
-        p2, = par2.plot(x_dat_p2, y_dat_p2, label=par2_data['data_name'], color=stl['color'],
-                        ls=stl['ls'], lw=stl['lw'], alpha=stl['alpha'])
+        try:
+            par2_inp = args.par2
+            par2 = host.twinx()
+            offset = 60
+            new_fixed_axis = par2.get_grid_helper().new_fixed_axis
+            par2.axis["right"] = new_fixed_axis(loc="right", axes=par2, offset=(offset, 0))  
+            par2.axis["right"].toggle(all=True)
+            par2_data = inp[par2_inp]
+            stl = styles[par2_inp[:4]]
+            par2.set_ylabel(par2_data['data_name'] + " (" + par2_data['unit'] + ")", color=stl['color'])
+            x_dat_p2, y_dat_p2 = xy_data(par2_data['data'])
+            p2_ymin, p2_ymax = expander(min(y_dat_p2), max(y_dat_p2), 0.075)
+            par2.set_ylim(p2_ymin, p2_ymax)
+            print("Plotting: " + par2_data['data_name'])
+            p2, = par2.plot(x_dat_p2, y_dat_p2, label=par2_data['data_name'], 
+            color=stl['color'],ls=stl['ls'], lw=stl['lw'], alpha=stl['alpha'])
+        except:
+            KeyError
+            if par2_inp != None:
+                print("Warning: Data block chosen for par2 does not exist!")
     if args.no_fractions:
         try:
             frac_data = inp['Fractions']['data']
@@ -231,7 +240,7 @@ def plotterX(inp,fname):
     host.legend(fontsize=8, fancybox=True, labelspacing=0.4, loc='upper right')
     host.xaxis.set_minor_locator(AutoMinorLocator())
     host.yaxis.set_minor_locator(AutoMinorLocator())
-    plt.title(fname, loc='left')
+    plt.title(fname, loc='left', size=8)
     internal_run_name = str(inp['Logbook']['run_name'])
     plot_file = fname[:-4] + "_" + internal_run_name + "_plot." + args.format
     plt.savefig(plot_file, bbox_inches='tight', dpi=args.dpi)
@@ -269,10 +278,10 @@ def data_writer1(fname, inp):
 'UV1_':{'color': '#1919FF', 'lw': 1.6, 'ls': "-", 'alpha':1.0},
 'UV2_':{'color': '#e51616', 'lw': 1.4, 'ls': "-", 'alpha':1.0},
 'UV3_':{'color': '#c73de6', 'lw': 1.2, 'ls': "-", 'alpha':1.0},
-'Cond':{'color': '#62181A', 'lw': 1.4, 'ls': "-", 'alpha':0.75},
+'Cond':{'color': '#FF7C29', 'lw': 1.4, 'ls': "-", 'alpha':0.75},
 'Conc':{'color': '#0F990F', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
-'Pres':{'color': '#3E1719', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
-'Temp':{'color': '#e04730', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
+'Pres':{'color': '#C0CBBA', 'lw': 1.0, 'ls': "-", 'alpha':0.50},
+'Temp':{'color': '#b29375', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
 'Inje':{'color': '#d56d9d', 'lw': 1.0, 'ls': "-", 'alpha':0.75},
 'pH':{'color': '#0C7F7F', 'lw': 1.0, 'ls': "-", 'alpha':0.75},}
 
@@ -297,4 +306,4 @@ def main2():
         if args.plot:
             plotterX(fdata, fname)
 
-main2()
+main2()

pycorn/pycorn.py

@@ -1,10 +1,9 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 '''
 PyCORN - script to extract data from .res (results) files generated
 by UNICORN Chromatography software supplied with ÄKTA Systems
 (c)2014-2015 - Yasar L. Ahmed
-v0.13
+v0.14
 '''
 
 from __future__ import print_function
@@ -218,6 +217,9 @@ def sensor_read(self, dat, show=False):
         for i in range(dat['adresse'] + 207, dat['adresse'] + 222, 15):
             s_unit = struct.unpack("15s", fread[i:i + 15])
             s_unit_dec = (codecs.decode(s_unit[0], 'iso8859-1')).rstrip('\x00')
+            # FIX: in some files the unit for temperature reads 'C' instead of '°C' 
+            if s_unit_dec == 'C':
+                s_unit_dec = u'°C'
         for i in range(dat['d_start'], dat['d_end'], 8):
             sread = struct.unpack("ii", fread[i:i + 8])
             data = round((sread[0] / 100.0) - self.inject_vol, 4), sread[1] / sensor_div
@@ -259,4 +261,4 @@ def load(self, show=False):
                 self[name] = dat
             else:
                 # TODO: Maybe we should keep this around?
-                del self[name]
+                del self[name]