Added initial file format documentation notebook, including example files.

Need better example files for R-T and for V-Phi

analysis_code/File format documentation and plotting routines.md

+---
+jupyter:
+  jupytext:
+    formats: ipynb,md
+    text_representation:
+      extension: .md
+      format_name: markdown
+      format_version: '1.2'
+      jupytext_version: 1.3.0
+  kernelspec:
+    display_name: Python 3
+    language: python
+    name: python3
+---
+
+```python
+import numpy as np
+import matplotlib.pyplot as plt
+```
+
+# Documentation of file formats
+
+In the document below, we include some documentation of the file formats generated by the SQUID practicum software, including some example plotting routines. 
+
+For more information on what is in the files and how it is generated, you can also have a look at the source code:
+
+https://gitlab.tudelft.nl/python-for-applied-physics/rp-squid-python-code/-/blob/master/SQUID%20measurement%20software.md
+
+Below, we document the four types of files generated by the software:
+
+* I-V data file
+* R-T data file
+* phi-V data file
+* PSD file
+
+
+## I-V data file
+
+Data in file generated from: 
+
+```
+np.savetxt(outname, np.array([t,I,V]).T)
+```
+
+The columns of the data file are:
+
+* **Column 0:** Sampling time of digitizer in seconds
+* **Column 1:** Applied current in $\mu$A
+* **Column 2:** Measured voltage in $\mu$V
+
+A recommended plot for documenting your data in a logbook:
+
+```python
+file =  "mrsquid_V-I_2020-10-16-12_05_03.dat"
+t,i,v = np.loadtxt(file, unpack=True)
+
+plt.subplots(figsize=(14,4))
+plt.subplot(121)
+plt.plot(t,v)
+plt.plot(t,i)
+plt.xlabel("Time (s)")
+plt.ylabel("I, V ($\mu$A, $\mu$V)")
+plt.axhline(0,ls=':',c='grey')
+plt.subplot(122)
+plt.plot(i,v)
+plt.axhline(0,ls=':',c='grey')
+plt.axvline(0,ls=':',c='grey')
+plt.xlabel("Applied current $I$ ($\mu$A)")
+plt.ylabel("Measured voltage $V$ ($\mu$A)")
+```
+
+## R-T data file
+
+Data in file generated from:
+
+```
+np.savetxt(outname, np.array([R,T,tm,Iavg,Iptp,Vavg,Vptp]).T)
+```
+
+* **Column 0:** Measured resistance from IV trace in Ohms (determined from linear fit)
+* **Column 1:** Measured temperature in Kelvin
+* **Column 2:** Measurement time in seconds since start of trace
+* **Column 3:** Averge applied current from IV trace
+* **Column 4:** Peak-to-peak applied current from IV trace
+* **Column 5:** Averge measured voltage from IV trace
+* **Column 6:** Peak-to-peak measured current from IV trace
+
+A recommended plot for documenting your data in a logbook:
+
+```python
+file =  "mrsquid_R_vs_T_2020-10-16-12_12_00.dat"
+R,T,tm,Iavg,Iptp,Vavg,Vptp = np.loadtxt(file, unpack=True)
+```
+
+```python
+plt.subplots(figsize=(12,10))
+plt.subplot(221)
+plt.plot(tm,R)
+plt.axhline(0,ls=':',c='grey')
+plt.xlabel("Measurement Time $t_m$ (s)")
+plt.ylabel("Measured Resistance $R$ (ohms)")
+plt.subplot(222)
+plt.plot(tm,T)
+plt.axhline(0,ls=':',c='grey')
+plt.xlabel("Measurement Time $t_m$ (s)")
+plt.ylabel("Measured Temperature (K)")
+plt.subplot(223)
+for name in "Iavg","Iptp":
+    d = eval(name)
+    plt.plot(tm,d,label=name)
+plt.axhline(0,ls=':',c='grey')
+plt.xlabel("Measurement Time $t_m$ (s)")
+plt.ylabel("Iavg,Iptp ($\mu$A)")
+plt.legend()
+plt.subplot(224)
+plt.plot(T,R)
+plt.ylabel("Measured Resistance $R$ (ohms)")
+plt.xlabel("Measured Temperature (K)")
+
+```
+
+# $\Phi$-V data file
+
+In $\Phi$-V mode, the magnetic flux in the loop is modulated by passing an current through the flux bias wire ("line").
+
+In practice, therefore, what is recorded is also a trace showing the measured voltage $V$ as a function of an applied current $I$. However, this applied current is passing through the flux bias line wire instead of the junctions themselves. 
+
+The file format is therefore the same, just the meaning of the axis labels are different:
+
+* **Column 0:** Sampling time of digitizer in seconds
+* **Column 1:** Flux bias current in $\mu$A
+* **Column 2:** Measured voltage in $\mu$V
+
+```python
+file =  "mrsquid_V-Phi_2020-10-16-12_05_03.dat"
+t,i,v = np.loadtxt(file, unpack=True)
+
+plt.subplots(figsize=(14,4))
+plt.subplot(121)
+plt.plot(t,v)
+plt.plot(t,i)
+plt.xlabel("Time (s)")
+plt.ylabel("I, V ($\mu$A, $\mu$V)")
+plt.axhline(0,ls=':',c='grey')
+plt.subplot(122)
+plt.plot(i,v)
+plt.axhline(0,ls=':',c='grey')
+plt.axvline(0,ls=':',c='grey')
+plt.xlabel("Flux bias current $I$ ($\mu$A)")
+plt.ylabel("Measured voltage $V$ ($\mu$A)")
+```
+
+# PSD data file
+
+In spectrum analyzer mode, the software calculates the power spectral density of the the two output channels of the 
+
+In practice, therefore, what is recorded is also a trace showing the measured voltage $V$ as a function of an applied current $I$. However, this applied current is passing through the flux bias line wire instead of the junctions themselves. 
+
+The file format is therefore the same, just the meaning of the axis labels are different:
+
+* **Column 0:** Frequency in Hz
+* **Column 1:** Current channel PSD $\mu$A$^2$/Hz
+* **Column 2:** Voltage channel PSD $\mu$V$^2$/Hz
+
+```python
+file = "mrsquid_PSD_2020-10-16-11_45_41.dat"
+f,Ipsd,Vpsd = np.loadtxt(file, unpack=True)
+
+plt.subplots(figsize=(14,6))
+plt.plot(f,Ipsd, label='Ipsd')
+plt.plot(f,Vpsd, label='Vpsd')
+plt.xlabel("Frequency (Hz)")
+plt.ylabel("Ipsd ($\mu$A$^2$/Hz), Vpsd ($\mu$V$^2$/Hz)")
+plt.legend()
+plt.yscale('log')
+plt.grid()
+```
+
+```python
+
+```