Update the forked lightlab

.gitignore

@@ -3,6 +3,7 @@
 dev-requirements-temp.txt
 test*.json
 labstate*.json
+.vscode
 
 # compiled data
 data/*

.travis.yml

@@ -1,7 +1,6 @@
 stages:
   - test
-  - name: deploy
-    if: branch = master AND tag IS present
+  - deploy
 
 stage: test
 language: python

CITATION.cff

@@ -0,0 +1,18 @@
+# YAML 1.2
+---
+abstract: "A python library for remote laboratory control."
+authors: 
+  -
+    family-names: Tait
+    given-names: Alex
+  -
+    family-names: "Ferreira de Lima"
+    given-names: Thomas
+cff-version: "1.1.0"
+date-released: 2019-06-28
+license: MIT
+message: "If you use this software, please cite it using these metadata."
+repository-code: "https://github.com/lightwave-lab/lightlab"
+title: Lightlab
+version: "1.0.7"
+...

Makefile

@@ -17,7 +17,7 @@ default: help ;
 
 venv: venv/bin/activate
 venv/bin/activate:
-	test -e venv/bin/activate || virtualenv -p python3 --prompt "(lightlab-venv) " --distribute venv
+	test -e venv/bin/activate || virtualenv -p python3 --prompt "(lightlab-venv) " venv
 	touch venv/bin/activate
 
 devbuild: venvinfo/devreqs~

README.rst

@@ -60,3 +60,7 @@ Server: Mac OS and Linux running ≥python3.6; not tested on Windows (to do).
 
 Auxiliary hosts: Mac OS, Linux, Windows
 
+Acknowledgements
+----------------
+
+This  material  is  based  in part upon  work  supported  by  the  National Science Foundation under Grant Number E2CDA-1740262. Any  opinions,  findings,  and  conclusions  or  recommendations expressed  in  this  material  are  those  of  the  author(s)  and  do  not necessarily reflect the views of the National Science Foundation.

docs/_static/misc/mergeWithNotebooks.md

@@ -8,13 +8,13 @@ Interactive tutorials are in notebooks. A full "experiment" in the lab is contai
 Jupyter notebooks have two sections: inputs (code, markdown) and outputs (stdout, plots, images). Interactive python notebook files embed compiled outputs. This is good if you want to restart a kernel but still see the output, or if you close the file, etc.
 
 ### Solution 1 and Problem 2: The nbstripout filter
-This is a cool thing that is integrated within the git commands. It basically ignores all of the outputs and metadata of `.ipynb` files. When you commit and push, it only pushes the inputs. It is installed via the requirements.txt, but there is also some interesting [discussion](https://stackoverflow.com/questions/18734739/using-ipython-notebooks-under-version-control/20844506) and [documentation](https://github.com/toobaz/ipynb_output_filter)
+`nbstripout` is a Git filter and "hides" the output and some metadata in `.ipynb` files from Git such that it does not get committed. This allows only tracking the actual input code cells in Git. It is installed via the `requirements.txt`, but there is also some interesting [discussion](https://stackoverflow.com/questions/18734739/using-ipython-notebooks-under-version-control/20844506) and [documentation](https://github.com/kynan/nbstripout)
 
 #### There are three downsides:
 1. What if you liked keeping those outputs without rerunning every commit?
 2. It has to strip evvverything, including all those high-quality graphics, every single time you `git status`.
 3. It crashes your essential commands. Very easy to get into a chicken-and-egg hole where you can't `diff` anything because __some__thing isn't JSON -- causing a crash -- but you can't figure out what isn't JSON because you can't see which files just changed.
-4. It corrupts your files. That's why we made cleannbline.
+4. It can corrupt files. That's why we made `cleannbline`.
 
 ### Solution 2. Deactivate the nbstripout filter
 
@@ -75,13 +75,13 @@ Run
 
     git status
 
-It takes some time. What is that error? It means that some of the notebooks are not sufficiently JSON for the nbstripout filter. 
+It takes some time. What is that error? It means that some of the notebooks are not valid JSON and cannot be parsed by the `nbstripout` filter. 
 
 In the crash log, it should point to a certain file, let's say `notebooks/Test.ipynb` First, clean it with
 
     ./cleannbline notebooks/Test.ipynb
 
-Then, open that file in Sublime and search for `<<<<`. Sometimes conflicts in your stash can get hidden in a way that does not show up in Jupyter. nbstripout will crash. You can find it in Sublime.
+Then, open that file in Sublime and search for `<<<<`. Sometimes conflicts in your stash can get hidden in a way that does not show up in Jupyter. `nbstripout` will crash. You can find it in Sublime.
 
 Return to running `git status` until it completes without error. It should show a ton of modifications: those are the effects of stripping. Add those and commit
 
@@ -95,13 +95,13 @@ Your filter is currently active, so when you try
 
 it will automatically crash. As above though, it will point to a file. Keep going until `git status` completes. Add those and commit.
 
-Side note: even though `git status` shows a ton of modifications, you should get a clean `git diff` (Although sometimes it will just crash, NBD). Both commands are applying the ipynb filter... in some way.
+Side note: even though `git status` shows a ton of modifications, you should get a clean `git diff` (Although sometimes it will just crash, NBD). Both commands are applying the `.ipynb` filter... in some way.
 
 #### Do the merge
     git checkout test_merge_cool-feature-into-development
     git merge cool-feature
 
-You will get conflicts in two categories: notebooks and other. Since there are `<<<<` things everywhere, your `git diff` will crash while you're in the merge. It also doesn't point you to an offending file. Here is where you'll really appreciate Sublime. 
+You will get conflicts in two categories: notebooks and other. Since there are `<<<<` conflict markers everywhere, your `git diff` will crash while you're in the merge. It also doesn't point you to an offending file. Here is where you'll really appreciate Sublime. 
 
 Make sure Sublime opens the entire `notebooks` _directory_. That way Find All will search all the files. 
 
@@ -116,7 +116,7 @@ Repeat for all the notebooks. Then do the same for all the regular code files. W
 
     git commit
 
-If for some reason, you want to escape the merge while keeping the test_merge branch stripped, you can run `git reset --hard`
+If for some reason, you want to abandon the merge while keeping the test_merge branch stripped, you can run `git reset --hard`
 
 #### Finalize
 Double check that everything went well (i.e. open some notebooks in Jupyter). If something screwed up in your merging _or_ stripping, you can just delete the test_merge branch and start over.

lightlab/equipment/abstract_drivers/TekScopeAbstract.py

@@ -1,5 +1,4 @@
 import numpy as np
-import pyvisa
 
 from lightlab import logger
 from lightlab.util.data import Waveform, FunctionBundle
@@ -154,7 +153,7 @@ def _triggerAcquire(self, timeout=None):
         if timeout is None:
             timeout = self.timeout / 1e3
         if timeout > 60:
-            logger.warning(f'Long timeout {timeout} specified, testing')
+            logger.warning('Long timeout %s specified, testing', timeout)
             old_avgCnt = self.timebaseConfig()['avgCnt']
             self.timebaseConfig(avgCnt=2)
             self._triggerAcquire(timeout=10)

lightlab/equipment/abstract_drivers/configurable.py

@@ -1,7 +1,7 @@
 from lightlab import visalogger as logger
 from pyvisa import VisaIOError
 from contextlib import contextmanager
-import dpath
+import dpath.util
 import json
 from numpy import floor
 from pathlib import Path
@@ -149,6 +149,7 @@ def transfer(self, source, subgroup=''):
             raise Exception('Invalid source for transfer. Got ' + str(type(source)))
         commands = sCon.getList(subgroup=subgroup)
         self.setList(commands)
+        return self
 
     @classmethod
     def fromFile(cls, fname, subgroup=''):

lightlab/equipment/abstract_drivers/electrical_sources.py

@@ -43,8 +43,8 @@ def _checkMode(cls, mode):
         '''
         if mode not in cls.supportedModes:
             raise TypeError('Invalid mode: ' + str(mode) + '. Valid: ' + str(cls.supportedModes))
-        else:
-            return mode.lower()
+
+        return mode.lower()
 
     @classmethod
     def val2baseUnit(cls, value, mode):

lightlab/equipment/lab_instruments/Agilent_N5222A_NA.py

@@ -198,7 +198,7 @@ def spectrum(self):
 
         self.setConfigParam('FORM', 'ASC')
         self.open()
-        dbm = self.mbSession.query_ascii_values('CALC{}:DATA? FDATA'.format(self.chanNum))
+        dbm = self.query_ascii_values('CALC{}:DATA? FDATA'.format(self.chanNum))
         self.close()
 
         fStart = float(self.getConfigParam('SENS:FREQ:STAR'))

lightlab/equipment/lab_instruments/Anritsu_MP1763B_PPG.py

@@ -1,6 +1,7 @@
 from . import VISAInstrumentDriver
 from lightlab.equipment.abstract_drivers import Configurable
 from lightlab.laboratory.instruments import PulsePatternGenerator
+from lightlab.util.data.one_dim import prbs_pattern
 import warnings
 import numpy as np
 import matplotlib.pyplot as plt
@@ -10,7 +11,7 @@ class Anritsu_MP1763B_PPG(VISAInstrumentDriver, Configurable):
     ''' ANRITSU MP1761A PulsePatternGenerator
         The PPG MP1763B at Alex's bench, which also support MP1761A (by Hsuan-Tung 07/27/2017)
 
-        Manual?
+        Manual (MP1763C):  http://www.otntech.com/modules/catalogue/download.php?id=52&mode=download&file_name=MP1763C.pdf
 
         Usage: :any:`/ipynbs/Hardware/PulsePatternGenerator.ipynb`
 
@@ -182,7 +183,8 @@ def bitseq(self, chpulses, clockfreq, ext=0, addplot=False, mult=1, res=5):
                 # delay channel (D=0) outputs the (P=N) set of pulses, the second min. delay channel (D=1)
                 # outputs the (P=N-1) set of pulses, etc.
                 # As a result, each pulse receives an inverse channel delay: K - current_delay + pulsePosition, for some K.
-                # We set K to max(delay) since that sets the last channel [max(delay)] at the beginning of the pattern.
+                # We set K to max(delay) since that sets the last channel [max(delay)] at
+                # the beginning of the pattern.
 
                 pIndex = int(np.round((max(chpulses.keys()) - delay + pulsePos) * clockfreq))
                 # add pulse to pattern at correct delay
@@ -206,3 +208,37 @@ def circ_time(T, pattern):
             plt.legend()
 
         return pattern
+
+    @classmethod
+    def PRBS_pattern(cls, order, mark_ratio=0.5):
+        # Documentation present in page 5-1 of the manual.
+        if mark_ratio != 0.5:
+            raise NotImplementedError("Only mark ratio of 1/2 is implemented so far.")
+
+        # The seed corresponds to the first digits in the bit sequence
+        # presented on the PPG (inverted order)
+        if order == 7:
+            polynomial = 0b10000011  # 1 + X^6 + X^7
+            seed = 0b1000000
+        elif order == 9:
+            polynomial = 0b1000010001  # 1 + X^5 + X^9
+            seed = 0b111100000
+        elif order == 11:
+            polynomial = 0b100000000101  # 1+X9+X11
+            seed = 0b11000000000
+        elif order == 15:
+            polynomial = 0b1000000000000011  # 1+X14+X15
+            seed = 0b000000000000001
+        elif order == 20:
+            polynomial = (1 << 20) + (1 << 20 - 3) + (1 << 20 - 20)  # 1+X3+X20
+            seed = 0b00111000111000111000
+        elif order == 23:
+            polynomial = (1 << 23) + (1 << 23 - 18) + (1 << 23 - 23)  # 1+X18+X23
+            seed = 0b1111100 << 16
+        elif order == 31:
+            polynomial = (1 << 31) + (1 << 31 - 28) + (1 << 31 - 31)  # 1+X28+X31
+            seed = 0b1110000 << 24
+        else:
+            raise NotImplementedError("PRBS{} not implemented.".format(order))
+
+        return prbs_pattern(polynomial, seed)

lightlab/equipment/lab_instruments/Apex_AP2440A_OSA.py

@@ -190,7 +190,14 @@ def transferData(self):
 
         dataLen = int(powerData[0])
         powerData = np.array(powerData[1:])
-        wavelengthData = np.linspace(self.wlRange[1], self.wlRange[0], dataLen)
+        retStr = self._query('SPDATAWL0')
+        wavelengthData = pyvisa.util.from_ascii_block(retStr,
+                                                      converter='f',
+                                                      separator=' ',
+                                                      container=list)
+        assert dataLen == wavelengthData[0]
+        wavelengthData = np.array(wavelengthData[1:])
+        # wavelengthData = np.linspace(self.wlRange[1], self.wlRange[0], dataLen)
 
         return wavelengthData[::-1], powerData[::-1]
 
@@ -205,7 +212,7 @@ def spectrum(self, average_count=1):
             self.triggerAcquire()
             nm, dbm = self.transferData()
 
-            if i is 0:
+            if i == 0:
                 dbmAvg = dbm / average_count
             else:
                 dbmAvg = dbmAvg + dbm / average_count