Issue76 improve scan save for qt3scan application

.gitignore

@@ -2,3 +2,5 @@ build/*
 .DS_Store
 *.egg-info
 *__pycache__
+*.ipynb_checkpoints
+.idea*

README.md

@@ -1,32 +1,92 @@
 # Utility Classes and Functions for the QT3 Lab
 
+This package provides a number of tools and fully-packaged programs for usage
+in the Quantum Technologies Teaching and Test-Bed (QT3) lab at the University of Washington.
+
+The QT3 lab confocal microscope utilizes the following hardware to perform
+various spin-control experiments on quantum systems, such as NV centers in diamond:
+
+ * TTL pulsers
+   * Quantum Composer Sapphire
+   * Spin Core PulseBlaster
+ * Excelitas SPCM for photon detection
+ * NI-DAQ card (PCIx 6363) for data acquisition and control
+ * Jena System's Piezo Actuator Stage Control Amplifier
+ * [Future] spectrometer
+
+The code in this package facilitates usages of these devices to perform
+experiments.
 
 # Setup
 
-### Requirements
+### Prerequisites
 
 The utilities in this package depend on publicly available Python packages found
-on PyPI and on packages developed in-house. This public packages will be installed
-automatically when you run the setup script (below). However, you will
-need to manually install the in-house packages
+on PyPI and on packages currently only on github. The public packages will be installed
+automatically when you run the installation script. However, you will first
+need to manually install the following packages
 
-* gadamc/qcsapphire
-* gadamc/qt3RFSynthControl
+* [gadamc/qcsapphire](https://github.com/gadamc/qcsapphire)
+* [gadamc/qt3RFSynthControl](https://github.com/gadamc/qt3RFSynthControl)
+* [gadamc/nipiezeojenapy](https://github.com/gadamc/nipiezeojenapy)
+* [zeeshawnkazi/pulseblaster](https://github.com/zeeshawnkazi/pulseblaster)
 
 ## Installation
 
+Once the prerequisite packages have been installed
+
 ```
-git clone https://github.com/gadamc/qt3nidaq-config
-cd qt3nidaq-config
+git clone https://github.com/gadamc/qt3-utils
+cd qt3-utils
 python -m pip install .
 ```
 
 # Usage
 
-In general, it's encouraged to supply usage instructions within
-the docstrings for the modules, classes and functions found in this package.
+The simplest way to get started is to see one of the [example](examples) notebooks.
+
+# Applications
+
+## QT3 Oscilloscope
+
+The console program `qt3scope` comes with this package. It allows you to run
+a simple program from the command-line that reads the count rate on a particular
+digital input terminal on the NI DAQ.
+
+Review the available command line options for the program. Pay special attention
+to the `--signal-terminal` option, ensuring that terminal value matches the current
+hardware setup.
+
+```
+> qt3scope --help
+```
+
+If default settings are correct, then should be able to run without options
 
-# Examples
+```
+> qt3scope
+```
+
+## QT3 Confocal Scan
+
+The console program `qt3scan` comes with this package.  This program launches
+a GUI applications that will perform a confocal scan using the Jena system
+piezo actuator.
+
+The run-time options available are very similar to `qt3scope`.
+Review the available command line options for the program. Pay special attention
+to the `--signal-terminal` option, ensuring that terminal value matches the current
+hardware setup.
+
+```
+> qt3scan --help
+```
+
+If default settings are correct, then should be able to run without options
+
+```
+> qt3scan
+```
 
 # Debugging