From d361fe8f5117c3c46586e3a42d7a3311467addea Mon Sep 17 00:00:00 2001
From: "Michael D. M. Dryden" <mdryden@chem.utoronto.ca>
Date: Wed, 22 Nov 2017 14:17:16 -0500
Subject: [PATCH 1/2] Add manual mode. Needs dstat-interface@1a40c83

---
 dstat_interface/core/experiments/chronoamp.py | 133 +++++++++++++++++-
 dstat_interface/core/interface/exp_int.py     |  59 +++++++-
 dstat_interface/core/interface/exp_window.py  |   1 +
 dstat_interface/main.py                       |   2 +
 4 files changed, 190 insertions(+), 5 deletions(-)

diff --git a/dstat_interface/core/experiments/chronoamp.py b/dstat_interface/core/experiments/chronoamp.py
index 5998178..56417cd 100644
--- a/dstat_interface/core/experiments/chronoamp.py
+++ b/dstat_interface/core/experiments/chronoamp.py
@@ -2,9 +2,12 @@ import time
 import struct
 import numpy as np
 import serial
+from copy import deepcopy
+
+from .experiment_template import PlotBox, Experiment, exp_logger, dstat_logger
 from ..interface.plot import mean, plotSpectrum, findBounds
+from ..dstat import state
 
-from .experiment_template import PlotBox, Experiment, exp_logger
 
 class ChronoampBox(PlotBox):
     def format_plots(self):
@@ -63,10 +66,132 @@ class Chronoamp(Experiment):
         
         if newline is True:
             self.data['current_time'].append(deepcopy(self.line_data))
+        try:
+            for i, item in enumerate(self.data['current_time'][line]):
+                item.append(data[i])
+        except IndexError:
+            pass
+
+class ManExp(Chronoamp):
+    id = 'man'
+    """Manual experiment"""
+    def setup(self):
+        self.handler_ids = [self.parameters['exp_window'].connect('new_voltage', self.new_voltage),
+                            self.parameters['exp_window'].connect('new_gain', self.new_gain)]
+
+        self.plots.append(ManBox('current_time'))
+
+        self.datatype = "linearData"
+        self.datalength = 2
+        self.databytes = 8
+        self.data = {'current_time': [([], [], [])]}
+        self.line_data = ([], [], [])
+        self.columns = ['Time (s)', 'Current (A)', 'Voltage (mV)']
+        self.plot_format = {
+            'current_time': {
+                'labels': self.columns,
+                'xlims': (0, 10)
+            }
+        }
+
+        self.commands.append("EN")
+
+    def new_voltage(self, widget, voltage):
+        state.ser.send_ctrl("v{}\n".format(int(voltage*(65536./3000)+32768)))
+
+    def new_gain(self, widget):
+        state.ser.send_ctrl("g{}\n".format(self.parameters['adc_pot'].params['gain']))
+
+    def serial_handler(self):
+        """Handles incoming serial transmissions from DStat. Returns False
+        if stop button pressed and sends abort signal to instrument. Sends
+        data to self.data_pipe as result of self.data_handler).
+        """
+
+        def check_ctrl():
+            if self.ctrl_pipe.poll():
+                input = self.ctrl_pipe.recv()
+                exp_logger.info("serial_handler: %s", input)
+                if input == "DISCONNECT":
+                    self.serial.write('a')
+                    self.serial.reset_input_buffer()
+                    exp_logger.info("serial_handler: ABORT pressed!")
+                    time.sleep(.3)
+                    return False
+                elif input == 'a':
+                    self.serial.write('a')
+                else:
+                    self.serial.write(input)
+
+        scan = 0
+        voltage = 0
+
+        try:
+            while True:
+                check_ctrl()
+
+                for line in self.serial:
+                    check_ctrl()
+
+                    if line.startswith('B'):
+                        data = self.data_handler(
+                            (scan, voltage, self.serial.read(size=self.databytes)))
+                        data = self.data_postprocessing(data)
+                        if data is not None:
+                            self.data_pipe.send(data)
+                        try:
+                            self.datapoint += 1
+                        except AttributeError:  # Datapoint counting is optional
+                            pass
+
+                    elif line.lstrip().startswith('S'):
+                        scan += 1
+
+                    elif line.lstrip().startswith('G'):
+                        self.gain = self.parameters["gain_table"][int(line.split(" ")[1])]
+
+                    elif line.lstrip().startswith('V'):
+                        voltage = int(line.split(" ")[1])
+
+                    elif line.lstrip().startswith("#"):
+                        dstat_logger.info(line.lstrip().rstrip())
+
+                    elif line.lstrip().startswith("@DONE"):
+                        dstat_logger.debug(line.lstrip().rstrip())
+                        time.sleep(.3)
+                        return True
+
+        except serial.SerialException:
+            return False
+
+    def data_handler(self, data_input):
+        """Overrides Experiment method to not convert x axis to mV."""
+        scan, voltage, data = data_input
+        # 2*uint16 + int32
+        seconds, milliseconds, current = struct.unpack('<HHl', data)
+        return (scan, (
+                       seconds+milliseconds/1000.,
+                       (current+self.gain_trim)*(1.5/self.gain/8388607),
+                       (voltage-32768)*(3000./65536)*self.re_voltage_scale
+                       )
+                )
+
+    def experiment_done(self):
+        """Runs when experiment is finished (all data acquired)"""
+        super(ManExp, self).experiment_done()
+        for i in self.handler_ids:
+            self.parameters['exp_window'].disconnect(i)
+
+class ManBox(ChronoampBox):
+    def redraw(self):
+        """Autoscale and refresh the plot. Overriden to scale both axes."""
+        for name, plot in self.subplots.items():
+            plot.relim()
+            plot.autoscale(True, axis='both')
+        self.figure.canvas.draw()
+
+        return True
 
-        for i, item in enumerate(self.data['current_time'][line]):
-            item.append(data[i])
-                
 class PDExp(Chronoamp):
     """Photodiode/PMT experiment"""
     id = 'pde'
diff --git a/dstat_interface/core/interface/exp_int.py b/dstat_interface/core/interface/exp_int.py
index 7235400..01e4f40 100755
--- a/dstat_interface/core/interface/exp_int.py
+++ b/dstat_interface/core/interface/exp_int.py
@@ -21,6 +21,7 @@ from __future__ import division, absolute_import, print_function, unicode_litera
 import os
 import sys
 import logging
+from collections import OrderedDict
 
 try:
     import gi
@@ -187,7 +188,63 @@ class Chronoamp(ExpInterface):
         
         for i in table:
             self.model.append(i)
-    
+
+
+class Manual(ExpInterface):
+    """Experiment class for Manual experiments."""
+    __gsignals__ = {
+        b'new_voltage': (GObject.SIGNAL_RUN_FIRST, None, (int, )),
+        b'new_gain': (GObject.SIGNAL_RUN_FIRST, None, ())
+    }
+    id = 'man'
+    experiment = chronoamp.ManExp
+
+    def __init__(self):
+        """Adds entry listings to superclass's self.entry dict"""
+        super(ExpInterface, self).__init__()  # initialize GObject
+        self.name = "Manual Mode"
+
+        self.entry = {}  # to be used only for str parameters
+        self._params = None
+
+        self.window = Gtk.ScrolledWindow()
+        self.window.set_vexpand(True)
+
+        grid = Gtk.Grid(orientation=Gtk.Orientation.VERTICAL)
+        grid.set_column_homogeneous(False)
+
+        entries = OrderedDict([
+            ('voltage', 'Voltage (mV)'),
+        ])
+
+        for n, i in enumerate(entries.items()):
+            key, value = i
+            grid.attach(Gtk.Label(label=value), 0, n, 1, 1)
+            self.entry[key] = Gtk.Entry()
+            grid.attach(self.entry[key], 1, n, 1, 1)
+
+        n += 1
+        voltage_button = Gtk.Button.new_with_label("Change Voltage")
+        grid.attach(voltage_button, 0, n, 2, 1)
+        voltage_button.connect('clicked', self.new_voltage)
+
+        n += 1
+        gain_button = Gtk.Button.new_with_label("Change Gain")
+        grid.attach(gain_button, 0, n, 2, 1)
+        gain_button.connect('clicked', self.new_gain)
+
+        self.window.add(grid)
+
+    def new_voltage(self, widget):
+        self.emit('new_voltage', int(self.entry['voltage'].get_text()))
+
+    def new_gain(self, widget):
+        self.emit('new_gain')
+
+    def get_window(self):
+        return self.window
+
+
 class LSV(ExpInterface):
     """Experiment class for LSV."""
     id = 'lsv'
diff --git a/dstat_interface/core/interface/exp_window.py b/dstat_interface/core/interface/exp_window.py
index d50405a..f34c108 100755
--- a/dstat_interface/core/interface/exp_window.py
+++ b/dstat_interface/core/interface/exp_window.py
@@ -87,6 +87,7 @@ class Experiments(GObject.Object):
     
     def setup_exp(self, parameters):
         exp = self.classes[self.expcombobox.get_active_id()]
+        parameters['exp_window'] = exp
         try:
             exp.param_test(parameters)
         except AttributeError:
diff --git a/dstat_interface/main.py b/dstat_interface/main.py
index b4a5b32..2080300 100755
--- a/dstat_interface/main.py
+++ b/dstat_interface/main.py
@@ -503,6 +503,8 @@ class Main(object):
                 params.set_params(self, param_override)
             
             parameters.update(params.get_params(self))
+            parameters['adc_pot'] = self.adc_pot
+            parameters['gain_table'] = dstat.state.board_instance.gain
             
             self.line = 0
             self.lastline = 0
-- 
GitLab


From 082ebee6cd08e3e992d5974338be9d96ed29ab95 Mon Sep 17 00:00:00 2001
From: Unknown <mdryden@chem.utoronto.ca>
Date: Wed, 22 Nov 2017 19:41:08 -0500
Subject: [PATCH 2/2] Desensitize manual controls while experiment not ready.

---
 dstat_interface/core/dstat/comm.py            |  4 ++--
 dstat_interface/core/dstat/dfu.py             |  1 +
 dstat_interface/core/experiments/chronoamp.py | 23 +++++++++++++------
 .../core/experiments/experiment_template.py   |  1 +
 dstat_interface/core/interface/exp_int.py     | 20 +++++++++++++++-
 dstat_interface/core/interface/exp_window.py  |  4 +++-
 dstat_interface/main.py                       |  2 +-
 7 files changed, 43 insertions(+), 12 deletions(-)

diff --git a/dstat_interface/core/dstat/comm.py b/dstat_interface/core/dstat/comm.py
index d78ea58..66903c8 100755
--- a/dstat_interface/core/dstat/comm.py
+++ b/dstat_interface/core/dstat/comm.py
@@ -192,7 +192,7 @@ class SerialConnection(GObject.Object):
         
     def get_proc(self, block=False):
         self.assert_connected()
-            
+
         if block is True:
             return self.proc_pipe_p.recv()
         else:
@@ -211,7 +211,7 @@ class SerialConnection(GObject.Object):
                 return self.ctrl_pipe_p.recv()
             else:
                 return None
-
+                
     def get_data(self, block=False):
         self.assert_connected()
         
diff --git a/dstat_interface/core/dstat/dfu.py b/dstat_interface/core/dstat/dfu.py
index 3b56288..101b9da 100755
--- a/dstat_interface/core/dstat/dfu.py
+++ b/dstat_interface/core/dstat/dfu.py
@@ -278,6 +278,7 @@ def test_firmware_version(current=None):
         logger.error('Unexpected git error. Git exited {}'.format(test))
         return False, None
 
+
 def dfu_program(path='./dstat-firmware.hex'):
     """Tries to program DStat over USB with DFU with hex file at path."""
     try:
diff --git a/dstat_interface/core/experiments/chronoamp.py b/dstat_interface/core/experiments/chronoamp.py
index 56417cd..bce5ecb 100644
--- a/dstat_interface/core/experiments/chronoamp.py
+++ b/dstat_interface/core/experiments/chronoamp.py
@@ -72,6 +72,7 @@ class Chronoamp(Experiment):
         except IndexError:
             pass
 
+
 class ManExp(Chronoamp):
     id = 'man'
     """Manual experiment"""
@@ -132,8 +133,8 @@ class ManExp(Chronoamp):
 
                 for line in self.serial:
                     check_ctrl()
-
-                    if line.startswith('B'):
+                    line_in = line.lstrip()
+                    if line_in.startswith('B'):
                         data = self.data_handler(
                             (scan, voltage, self.serial.read(size=self.databytes)))
                         data = self.data_postprocessing(data)
@@ -144,19 +145,22 @@ class ManExp(Chronoamp):
                         except AttributeError:  # Datapoint counting is optional
                             pass
 
-                    elif line.lstrip().startswith('S'):
+                    elif line_in.startswith('S'):
                         scan += 1
 
-                    elif line.lstrip().startswith('G'):
+                    elif line_in.startswith('G'):
                         self.gain = self.parameters["gain_table"][int(line.split(" ")[1])]
 
-                    elif line.lstrip().startswith('V'):
+                    elif line_in.startswith('V'):
                         voltage = int(line.split(" ")[1])
 
-                    elif line.lstrip().startswith("#"):
+                    elif line_in.startswith("#"):
                         dstat_logger.info(line.lstrip().rstrip())
 
-                    elif line.lstrip().startswith("@DONE"):
+                    elif line_in.startswith("R"):
+                        self.ctrl_pipe.send("R")
+
+                    elif line_in.startswith("@DONE"):
                         dstat_logger.debug(line.lstrip().rstrip())
                         time.sleep(.3)
                         return True
@@ -164,6 +168,10 @@ class ManExp(Chronoamp):
         except serial.SerialException:
             return False
 
+    def ctrl_loop(self, data):
+        if data == 'R':
+            self.emit('exp_ready')
+
     def data_handler(self, data_input):
         """Overrides Experiment method to not convert x axis to mV."""
         scan, voltage, data = data_input
@@ -181,6 +189,7 @@ class ManExp(Chronoamp):
         super(ManExp, self).experiment_done()
         for i in self.handler_ids:
             self.parameters['exp_window'].disconnect(i)
+        self.emit('exp_done')
 
 class ManBox(ChronoampBox):
     def redraw(self):
diff --git a/dstat_interface/core/experiments/experiment_template.py b/dstat_interface/core/experiments/experiment_template.py
index bd36ce5..9fab05d 100755
--- a/dstat_interface/core/experiments/experiment_template.py
+++ b/dstat_interface/core/experiments/experiment_template.py
@@ -69,6 +69,7 @@ class Experiment(GObject.Object):
         b'exp_ready': (GObject.SIGNAL_RUN_FIRST, None, ()),
         b'exp_done': (GObject.SIGNAL_RUN_FIRST, None, ())
     }
+
     def __init__(self, parameters):
         """Adds commands for gain and ADC."""
         super(Experiment, self).__init__()
diff --git a/dstat_interface/core/interface/exp_int.py b/dstat_interface/core/interface/exp_int.py
index 4a68475..6f26ece 100755
--- a/dstat_interface/core/interface/exp_int.py
+++ b/dstat_interface/core/interface/exp_int.py
@@ -214,7 +214,7 @@ class Manual(ExpInterface):
         self.window.set_vexpand(True)
 
         grid = Gtk.Grid(orientation=Gtk.Orientation.VERTICAL)
-        grid.set_column_homogeneous(False)
+        grid.set_column_homogeneous(True)
 
         entries = OrderedDict([
             ('voltage', 'Voltage (mV)'),
@@ -236,8 +236,26 @@ class Manual(ExpInterface):
         grid.attach(gain_button, 0, n, 2, 1)
         gain_button.connect('clicked', self.new_gain)
 
+        self.buttons = [voltage_button, gain_button]
+        for i in self.buttons:
+            i.set_sensitive(False)
+
         self.window.add(grid)
 
+    def exp_ready(self, widget):
+        for i in self.buttons:
+            i.set_sensitive(True)
+
+    def exp_done(self, widget):
+        for i in self.buttons:
+            i.set_sensitive(False)
+
+    def get_experiment(self, parameters):
+        exp = super(Manual, self).get_experiment(parameters)
+        exp.connect('exp_ready', self.exp_ready)
+        exp.connect('exp_done', self.exp_done)
+        return exp
+
     def new_voltage(self, widget):
         self.emit('new_voltage', int(self.entry['voltage'].get_text()))
 
diff --git a/dstat_interface/core/interface/exp_window.py b/dstat_interface/core/interface/exp_window.py
index 9f7f25a..9f977da 100755
--- a/dstat_interface/core/interface/exp_window.py
+++ b/dstat_interface/core/interface/exp_window.py
@@ -33,11 +33,13 @@ from . import exp_int
 
 logger = logging.getLogger(__name__)
 
+
 class Experiments(GObject.Object):
     __gsignals__ = {
         'run_utility': (GObject.SIGNAL_RUN_FIRST, None, ()),
         'done_utility': (GObject.SIGNAL_RUN_FIRST, None, ())
     }
+
     def __init__(self, builder):
         super(Experiments,self).__init__()
         self.builder = builder
@@ -96,7 +98,7 @@ class Experiments(GObject.Object):
                     exp.name)
                 )
         return exp.get_experiment(parameters)
-
+    
     def hide_exps(self):
         for key in self.containers:
             self.containers[key].hide()
diff --git a/dstat_interface/main.py b/dstat_interface/main.py
index ff49410..febd0ba 100755
--- a/dstat_interface/main.py
+++ b/dstat_interface/main.py
@@ -640,7 +640,7 @@ class Main(object):
                     self.current_exp.ctrl_loop(ctrl_buffer)
             except AttributeError:
                 pass
-            
+
             proc_buffer = dstat.state.ser.get_proc()
             if proc_buffer is not None:
                 if proc_buffer in ["DONE", "SERIAL_ERROR", "ABORT"]:
-- 
GitLab