Adding an informative README

UserTools/PMTWaveformSim/README.md

@@ -1,20 +1,22 @@
-# PMTWaveformSim
-
-PMTWaveformSim
-
-## Data
-
-Describe any data formats PMTWaveformSim creates, destroys, changes, or analyzes. E.G.
-
-**RawLAPPDData** `map<Geometry, vector<Waveform<double>>>`
-* Takes this data from the `ANNIEEvent` store and finds the number of peaks
+# PMTWaveformSim
 
-
-## Configuration
-
-Describe any configuration variables for PMTWaveformSim.
-
-```
-param1 value1
-param2 value2
-```
+PMTWaveformSim generates PMT waveforms based on the simulated PMT hits. For each MCHit a lognorm waveform is sampled based on fit parameters extracted from SPE waveforms in data. The fit parameters are randomly sampled in a way that conserved the covariance between parameters and captures the random behavior of a PMT's response. A full extended readout window (70 us) is sampled and waveforms from overlapping hits are added. A random baseline between 300 and 350 ADC is added. Random noise is applied, where the noise sigma is sampled from a gaussian with mean 1 and std dev of 0.25. The baseline and noise envelope values are hardcoded at the moment. Finally, any ADC counts above 4095 are clipped to mimick saturation. 
+
+## Data
+
+**RawADCDataMC** `std::map<unsigned long, std::vector<MCWaveform<uint16_t>> >`
+* The raw simulated waveforms. The key is PMT channel number, then inner vector should always have size == 1
+
+**CalibratedADCData** `std::map<unsigned long, std::vector<CalibratedADCWaveform<double>> >`
+* The "calibrated" simulated waveforms. The baseline and sigma are the true, randomly-generated values. The key is PMT channel number, then inner vector should always have size == 1
+
+
+## Configuration
+
+```
+PMTParameterFile configfiles/PMTWaveformSim/PMTWaveformLognormFit.csv # file containing the fit parameters and triangular Cholesky decomposed covariance matrix
+Prewindow 10 # number of clock ticks before the MC hit time to begin sampling the fit function
+ReadoutWindow 35 # number of clock ticks around the MC hit time over which waveforms are sampled
+T0Offset 0 # A timing offset (in clock ticks) that can be used to align the pulse start time
+MakeDebugFile 0 # Produce a root file containing all the simulated waveforms
+```