Updated docs

Author: pyahmed

README.rst

@@ -6,12 +6,13 @@ 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 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).
+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.
+
+Installation:
+
+- pip install pycorn
 
 Limitations:
 
@@ -24,7 +25,9 @@ Requirements:
 
 Usage:
 
-- See docs/USAGE.txt
+- 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
+
 
 License:
 

docs/CHANGES.txt

@@ -1,3 +1,10 @@
+v0.13
+======
+- Conversion to of PyCORN to class-structure, allows using PyCORN in other scripts (by Wendell Smith)
+- Plots are now UV + user selectable 2nd/3rd data block (2nd y-axis is Conductivity by default)
+- Made some changes to adapt for PyPI
+- Installation should place pycorn-bin.py in Python/Scripts-folder
+
 v0.12
 ======
 - Logbook is extracted and written to txt-file

docs/USAGE.txt docs/USAGE_pycorn-bin.txtdocs/USAGE.txt renamed to docs/USAGE_pycorn-bin.txt

@@ -1,5 +1,12 @@
 How to use PyCORN
-=================
+
+PyCORN may be used either via the pycorn-bin.py-script or imported as a module in your scripts (see USAGE_pycorn_module.txt).
+
+pycorn-bin.py:
+--------------
+The default installation places pycorn-bin.py in the python/scripts-folder and therefor ready-to-use on most platforms. This script re-implements most of the features of the original pycorn.py-script. Usage is very similar, as only a few paramters have changed. 
+
+
 usage: pycorn-bin.py [-h] [-c] [-n] [-i #] [-r #] [-t] [-e] [-p]
                      [--no_fractions] [--xmin #] [--xmax #] [--par1 PAR1]
                      [--par2 PAR2]
@@ -46,26 +53,26 @@ z,tif,tiff,jpg,jpeg,png,ps,eps,raw,rgba,pdf,pgf}
                         etc.). Default is 300.
 
 Notes:
-By default PyCORN will plot from first to last fraction, as that is usually the interesting part. If no fractions are present in the run then from beginning to end. To override this behaviour you can use the (both) optional --xmin/--xmax switches to specify beginning and of the plot.
+By default pycorn-bin.py will plot from first to last fraction, as that is usually the interesting part. If no fractions are present in the run then from beginning to end. To override this behaviour you can use the (both) optional --xmin/--xmax switches to specify beginning and end of the plot.
 
 Examples:
 Show user who ran method:
-pycorn.py -u input.res
+pycorn-bin.py -u input.res
 
 Show injection points:
-pycorn.py -t input.res
+pycorn-bin.py -t input.res
 
 Extract data to csv files:
-pycorn.py -e input.res
+pycorn-bin.py -e input.res
 
 Plot all data:
-pycorn.py -p input.res
+pycorn-bin.py -p input.res
 
 Extract/plot data and adjust retention volume to injection point 1 (counting starts at 0!):
-pycorn.py -p -e -i 1 input.res
+pycorn-bin.py -p -e -i 1 input.res
 
 Plot every third value:
-pycorn.py -p -r 3 input.res
+pycorn-bin.py -p -r 3 input.res
 
 Plot from 100 to 200ml:
-pycorn.py -p --xmin 100 --xmax 200 input.res
+pycorn-bin.py -p --xmin 100 --xmax 200 input.res

docs/USAGE_pycorn_module.txt

@@ -0,0 +1,34 @@
+Using the pycorn module:
+
+# Importing the module
+from pycorn import pc_res3
+
+# Create an instance of the pycorn object, there are a couple of options that can be specified: 
+#     file_name = file name of the res-file that you want to load
+#     reduce = integer to only read every n sample (similar to the option found in UNICORN during export to asc)
+#     inj_sel = which injection point to use as zero-rentention. By default the last injection point is used (same as in UNICORN)
+
+# Create the instance using default options
+my_res_file = pc_res3("sample1.res")
+
+# Parse the file
+my_res_file.load()
+
+# Show available data
+print(list(my_res_file.keys()))
+
+>>>[u'CreationNotes', u'Logbook', u'UV', u'Cond', u'pH', u'Pressure', u'Temp', u'Conc', u'Fractions']
+
+# The above list is your key to access the data inside the file
+# my_res_file[key][value] value can be:
+#   data: contains the actual data, either pure text or a list with x/y-pairs as tuples
+#   unit: the unit for this data block (mAu, ms/cm etc.)
+#   run_name: an internal name (like "Manual Run 8")
+
+# For example to read-out the the unit for the UV-block:
+my_res_file['UV']['unit']
+
+# To read the actual UV-data:
+x = my_res_file['UV']['data']
+print(x[0:3])
+>>>[(0.0, -9.22), (0.06, -0.007), (0.13, -0.004)]