Web app

CHANGES.txt

@@ -1,2 +1,4 @@
-V0.1.2a, Dec 14, 2014 -- First Conda Package
+V0.2.1,  Jan 12, 2017 -- Added place_server
+V0.2.0,  Jan 12, 2017 -- Web Inerface Added
+V0.1.2a, Dec 14, 2016 -- First Conda Package
 V0.1.0,  May 28, 2014 -- Initial release

README.txt → README.md

@@ -1,21 +1,44 @@
 
-=====
-PLACE 
-=====
+# PLACE 
 
 PLACE is an open-source Python package for laboratory automation, control, and experimentation.  
 
 It provides driver modules for automating laboratory instruments, example implementation scripts, and modules for visualizing and processing waveform data (available with PALplots: https://github.com/PALab/PALplots).
 
 A goal of PLACE is to develop a repository of instrument drivers for laboratory automation.  In addition, rapid development of compatible processing software will streamline laboratory activity from acquisition through data analysis.
 
-To install PLACE from the source:
-Download the source code and unzip `PLACE-master.zip`.  From the `PLACE-master` folder, run the following from the command line to install:
+## Installation
 
-python setup.py install
+### Install PLACE via conda
 
+```
+conda install -c defaults -c conda-forge -c freemapa place
+pip install obspyh5 websockets
+```
+
+## Running PLACE
+
+### Control PLACE via the command-line interface
+
+```
+place_scan [options]
+```
+
+Run ```scan --help``` for options.
+
+### Control PLACE via web app (requires Python >= 3.5)
+
+```
+place_server
+```
+
+Then open place/web/place.html in any web browser.
+
+## Authors
 
-Authors:
 Jami L Johnson
+
 Henrik tom Wörden
+
 Kasper van Wijk
+

docs/conf.py

@@ -63,9 +63,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.1'
+version = u'0.2'
 # The full version, including alpha/beta/rc tags.
-release = u'0.1.2a'
+release = u'0.2.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -139,7 +139,7 @@
 # The name for this set of Sphinx documents.
 # "<project> v<release> documentation" by default.
 #
-# html_title = u'PLACE v0.1.2a'
+# html_title = u'PLACE v0.2.1'
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #

meta.yaml

@@ -1,17 +1,17 @@
 package:
     name: place
-    version: "0.1.2a"
+    version: "0.2.1"
 
 source:
     path: .
 
 requirements:
     build:
-        - python >=2.7
+        - python
         - setuptools
 
     run:
-        - python >=2.7
+        - python
         - httplib2
         - obspy
         - numpy >=1.0.0

place/automate/scan/scanFunctions.py

@@ -321,7 +321,7 @@ def options(self,opts,args):
         for o, a in opts:
             if o in ('-h', '--help'):
                 print(__doc__)
-                sys.exit(0)
+                return
             if o in ("--n"):
                 filename = a + '.h5'
             if o in ("--n2"):

place/scripts/scan.py

@@ -18,6 +18,13 @@
 
 import sys
 import os
+import time
+from math import ceil, log
+import signal
+import getopt
+import re
+import shlex
+import functools
 
 # set permissions of RS-232 serial port for vibrometer control
 # (removed in favour of using proper permissions -Paul Freeman)
@@ -28,19 +35,14 @@
 #os.system('sudo chmod -R 0777 /dev/ttyUSB0') # laser
 #os.system('sudo chmod a+rw /dev/ttyUSB0')
 
-from math import ceil, log
-import matplotlib.pyplot as plt 
+import matplotlib.pyplot as plt
 import numpy as np
 from numpy import matrix
-import getopt
-import time
 from obspy import read, Trace, UTCDateTime
 from obspy.core.trace import Stats
 from obspy.core import AttribDict
-import re
 import h5py
 import obspyh5
-from time import sleep
 
 # PLACE modules
 import place.automate.osci_card.controller as card
@@ -61,60 +63,64 @@
     import pickle
 
 from place.automate.quanta_ray.QRay_driver import QuantaRay
-from place.automate.scan.scanFunctions import Initialize, Execute, Scan 
+from place.automate.scan.scanFunctions import Initialize, Execute, Scan
 
-def main():
+global instruments, par
+instruments = []
+par = []
 
+def main(args_in=sys.argv):
+    try:
+        process_args(args_in)
+    except KeyboardInterrupt:
+        print('Keyboard Interrupt!  Instrument connections closing...')
+        Execute().close(instruments,par)
+
+def process_args(args_in):
     # -----------------------------------------------------
     # process command line options
     # -----------------------------------------------------
-
-    # check if server-mode has been requested
-    if sys.argv[1] == "--serve":
-        scan_server()
-
     try:
-
-        opts,args = getopt.getopt(sys.argv[1:], 'h',['help','s1=','s2=','scan=','dm=','sr=','tm=','ch=','ch2=','av=','wt=','rv=','ret=','sl=','vch=','tl=','tr=','cr=','cr2=','cp=','cp2=','ohm=','ohm2=','i1=','d1=','f1=','i2=','d2=','f2=','n=','n2=','dd=','rg=','map=','en=','lm=','rr=','pp=','bp=','so=','comments='])
+        opts,args = getopt.getopt(args_in[1:], 'h',['help','s1=','s2=','scan=','dm=','sr=','tm=','ch=','ch2=','av=','wt=','rv=','ret=','sl=','vch=','tl=','tr=','cr=','cr2=','cp=','cp2=','ohm=','ohm2=','i1=','d1=','f1=','i2=','d2=','f2=','n=','n2=','dd=','rg=','map=','en=','lm=','rr=','pp=','bp=','so=','comments='])
 
     except getopt.error as msg:
         print(msg)
         print('for help use --help')
-        sys.exit(_SCAN_FAILURE_INVALID_ARUGMENTS)
-
-    global instruments, par 
+        sys.exit(1)
 
     par = Initialize().options(opts, args)
-
+    if par == None:
+        return
+
     # -----------------------------------------------------
     # Initialize instruments
     # -----------------------------------------------------
-    
+
     instruments = []
- 
+
     # Initialize stage or mirrors for each dimension
-  
+
     if par['SCAN'] == '1D':
         if par['GROUP_NAME_1'] == 'PICOMOTOR-X' or par['GROUP_NAME_1'] == 'PICOMOTOR-Y':
             par = Initialize().picomotor_controller('130.216.58.155',23,par)
-            
+
         else:
             par = Initialize().controller('130.216.58.154',par,1)
         instruments.append(par['GROUP_NAME_1'])
-    
+
     elif par['SCAN'] == '2D' or par['SCAN'] == 'dual':
         if par['GROUP_NAME_1'] in ['PICOMOTOR-X','PICOMOTOR-Y']:
             par = Initialize().picomotor_controller('130.216.58.155',23,par)
         else:
             par = Initialize().controller('130.216.58.154',par,1)
-        instruments.append(par['GROUP_NAME_1'])     
-        if par['GROUP_NAME_2'] in ['PICOMOTOR-X','PICOMOTOR-Y']: 
+        instruments.append(par['GROUP_NAME_1'])
+        if par['GROUP_NAME_2'] in ['PICOMOTOR-X','PICOMOTOR-Y']:
             par = Initialize().picomotor_controller('130.216.58.155',23,par)
         else:
-            par = Initialize().controller('130.216.58.154',par,2)  
+            par = Initialize().controller('130.216.58.154',par,2)
         print(par['GROUP_NAME_2'])
         instruments.append(par['GROUP_NAME_2'])
-          
+
     # Initialize and set header information for receiver
     if par['RECEIVER'] == 'polytec':
         par = Initialize().polytec(par)
@@ -167,7 +173,7 @@ def main():
     # -----------------------------------------------------
     # Perform scan
     # -----------------------------------------------------
-        
+
     if par['SCAN'] == '1D':
         Scan().oneD(par, header)
     elif par['SCAN'] == '2D':
@@ -183,22 +189,19 @@ def main():
     # close instrument connections
     # -----------------------------------------------------
     Execute().close(instruments,par)
-   
-    sys.exit(_SCAN_SUCCESS)
+
+    sys.exit(0)
 
 
 
 # wait for requests
-def scan_server():
-    """*In development.* Starts a websocket server to listen for scan requests.
+def scan_server(port=9130):
+    """Starts a websocket server to listen for scan requests.
 
-    This function will be used to initiate a special scan process. Rather
+    This function is used to initiate a special scan process. Rather
     than specify the parameters via the command-line, this mode waits
     for scan commands to arrive via a websocket.
 
-    Currently, the function will simply print the message it received
-    locally and return a message to the sender.
-
     Once this server is started, it will need to be killed via ctrl-c or
     similar.
 
@@ -213,58 +216,49 @@ def scan_server():
         print()
         print("    pip install websockets")
         print()
-        sys.exit(_SCAN_FAILURE_MISSING_MODULE)
-
+        sys.exit(1)
     try:
         import asyncio
     except ImportError:
         print("Running as server requires the asyncio module")
         print("but asyncio cannot be imported.")
         print()
-        sys.exit(_SCAN_FAILURE_MISSING_MODULE)
-
-    async def scan_socket(websocket, path):
-        """Creates an asyncronous websocket to listen for scans.
+        sys.exit(1)
 
-        Use of this function is handled internally by the application.
+    def ask_exit():
+        """Signal handler to catch ctrl-c (SIGINT) or SIGTERM"""
+        loop.stop()
 
-        Note:
-            This function is created dynamically due to the fact that it
-            makes use of Python 3.5 libraries.
-        """
+    async def scan_socket(websocket, path):
+        """Creates an asyncronous websocket to listen for scans."""
+        print("Starting websockets server on port {}".format(port))
         # get a scan command from the webapp
         request = await websocket.recv()
-
-        #TODO make this actually call the main function
-        print("This is what I would like to run:")
+        print("This is what I am running:")
         print(request)
-
+        process_args(shlex.split(request))
         # send message back to the webapp
         await websocket.send("Scan received")
 
-    scan_server_port = 9130
-    start_server = websockets.serve(
-            scan_socket,
-            'localhost',
-            scan_server_port)
-    print("Starting websockets server at ws://localhost:{}"
-            .format(scan_server_port))
-
-    asyncio.get_event_loop().run_until_complete(start_server)
-    asyncio.get_event_loop().run_forever()
+    loop = asyncio.get_event_loop()
+    # set up signal handlers
+    for signame in ('SIGINT', 'SIGTERM'):
+        loop.add_signal_handler(getattr(signal, signame), ask_exit)
+    coroutine = websockets.server.serve(scan_socket, 'localhost', port)
+    # run websocket server
+    server = loop.run_until_complete(coroutine)
+    loop.run_forever()
+    # cleanup
+    server.close()
+    loop.run_until_complete(server.wait_closed())
+    loop.close()
 
 
 
 if __name__ == "__main__":
-    try:
-        while(True):
-            main()
-    except KeyboardInterrupt:
-        print('Keyboard Interrupt!  Instrument connections closing...')
-        Execute().close(instruments,par)
-
-# exit codes
-_SCAN_SUCCESS                   = 0
-_SCAN_FAILURE_MISSING_MODULE    = 1
-_SCAN_FAILURE_INVALID_ARUGMENTS = 2
+    # check if server-mode has been requested
+    if sys.argv[1] == "--serve":
+        scan_server()
+    else:
+        main(sys.argv)
 

place/web/elm-package.json

@@ -1,5 +1,5 @@
 {
-    "version": "0.1.0",
+    "version": "0.2.1",
     "summary": "webapp for interfacing with PLACE",
     "repository": "https://github.com/PALab/place.git",
     "license": "LGPLv3",