Merge pull request #59 from CardiacModelling/MichaelClerx-patch-1

Update README.md with much more detailed instructions

Author: MichaelClerx

README.md

@@ -19,13 +19,15 @@ cd pcpostprocess
 Create and activate a virtual environment.
 
 ```sh
-python3 -m venv .venv && source .venv/bin/activate
+python3 -m venv .venv
+source .venv/bin/activate
 ```
 
 Then install the package with `pip`.
 
 ```sh
-python3 -m pip install --upgrade pip && python3 -m pip install -e .'[test]'
+python3 -m pip install --upgrade pip
+python3 -m pip install -e .'[test]'
 ```
 
 To run the tests you must first download some test data.
@@ -111,3 +113,138 @@ options:
   --log_level LOG_LEVEL
 ```
 
+## Example: Running on test data
+
+Once the tests have completed, you can try out the program on the downloaded test data.
+
+This data is organised as follows:
+
+```
+13112023_MW2_FF
+ |- StaircaseInStaircaseramp (2)_2kHz_15.01.51
+ |- StaircaseInStaircaseramp (2)_2kHz_15.12.17
+ |- staircaseramp (2)_2kHz_15.01.07
+ |- staircaseramp (2)_2kHz_15.06.53
+ |- staircaseramp (2)_2kHz_15.11.33
+ |- staircaseramp (2)_2kHz_15.17.19
+ |- export_config.py
+```
+
+To make sense of this data set, pcpostprocess requires the file `export_config.py` to be present.
+For the example data, this contains
+
+```
+#
+# Config for export
+#
+
+# Copy this config file to the main directory of data
+
+# E.g. path to the main directory of data
+# /run/media/cholei/Chon/Adam_Syncropatch_May_2019/20190314MPAN
+
+# Data output directory
+savedir = './data'
+
+# Save name for this set of data
+saveID = '13112023_MW2'
+
+# DataControl384 protocol output names to shorter names
+# For QC only
+D2S_QC = {
+    'staircaseramp (2)_2kHz': 'staircaseramp'
+}
+
+# For export only
+D2S = {
+    'staircaseramp (2)_2kHz': 'staircaseramp',
+    'staircaseramp1': 'staircaseramp1',
+    'staircaseramp2': 'staircaseramp2',
+    'StaircaseInStaircaseramp': 'sis',
+    'hhbrute3gstep': 'hhbrute3gstep',
+    'hhsobol3step': 'hhsobol3step',
+    'wangbrute3gstep': 'wangbrute3gstep',
+    'wangsobol3step': 'wangsobol3step',
+    'longAPs (2)': 'longap',
+    'StaircaseInStaircaserampInverse': 'sisi',
+    'squarewave': 'squarewave',
+    'maxdiff': 'maxdiff',
+#    'ManualPhasPlaneExploration': 'manualppx',
+    'random-t-optimised-v': 'rtov',
+    'random-v-optimised-t': 'rvot',
+    'SpaceFillingProtocol10': 'spacefill10',
+    'SpaceFillingProtocol19': 'spacefill19',
+    'SpaceFillingProtocol26': 'spacefill26',
+    'StaircaseInStaircaseramp': 'sis'
+}
+
+# I-V like protocols, their format so is, different need to be treated in
+# slightly different way
+IVProtocolList = [
+    ]
+
+# Protocols that have been run twice (most probably for stability check)
+# Note that not repeats within the same 'protocol'
+RepeatedProtocolList = [
+    'staircaseramp1',
+    'staircaseramp2',
+    'sis',
+    'hhbrute3gstep',
+    'hhsobol3step',
+    'wangbrute3gstep',
+    'wangsobol3step',
+    'longap',
+    'sisi',
+    'squarewave',
+    'maxdiff',
+    'manualppx',
+    'rvot',
+    'rtov',
+    'spacefill10',
+    'spacefill19',
+    'spacefill26',
+    'sis'
+]
+```
+
+
+Instead of running on all wells (which takes about an hour to complete), we'll run on just two wells:
+```
+pcpostprocess run_herg_qc ./tests/test_data/13112023_MW2_FF/ -w A02 A03
+```
+This should take around 5 minutes to run, and produce the following output
+output
+ |- hergqc
+     |- 13112023_MW2-staircaseramp_2-leak_fit-after
+     |- 13112023_MW2-staircaseramp_2-leak_fit-before
+     |- 13112023_MW2-staircaseramp-leak_fit-after
+     |- 13112023_MW2-staircaseramp-leak_fit-before
+     |- debug
+     |- leak_correction
+     |- output
+     |- reversal_plots
+     |- subtraction_plots
+     |- traces
+     |- A02-sweep0-after.png
+     |- A02-sweep0-before.png
+     |- A02-sweep1-after.png
+     |- A02-sweep1-before.png
+     |- A03-sweep0-after.png
+     |- A03-sweep0-before.png
+     |- A03-sweep1-after.png
+     |- A03-sweep1-before.png
+     |- chrono.txt
+     |- info.txt
+     |- passed_wells.txt
+     |- QC-13112023_MW2.csv
+     |- QC-13112023_MW2.json
+     |- qc_table.tex
+     |- qc_table.xlsx
+     |- qc_vals_df.csv
+     |- selected-13112023_MW2.txt
+     |- selected-13112023_MW2-staircaseramp.txt
+     |- selected-13112023_MW2-staircaseramp_2.txt
+     |- subtraction_qc.csv
+```
+
+Here ...