class itkBinaryImageMorphologyInputSpec(CommandLineInputSpec):
inFilename = File(argstr='%s',
desc="inFilename",
exists=True,
mandatory=True,
position=0)
fileMode = traits.Str(argstr='%s',
desc="fileMode",
exists=True,
mandatory=True,
position=1)
var1 = traits.String(argstr='%s',
desc="var1",
exists=True,
mandatory=True,
position=2)
var2 = traits.String(argstr='%s',
desc="var2",
exists=True,
mandatory=True,
position=3)
radius = traits.List(argstr='%s',
type="traits.Float",
sep=",",
desc="radius",
exists=True,
mandatory=True,
position=4)
outFilename = traits.Str(argstr='%s',
desc="outFilename",
exists=True,
mandatory=True,
position=5)
def __init__(self, fname=""):
self.data = eta.Dict()
self.fname = eta.File()
self.plotting = eta.String()
self.open_VERT = eta.Button("Open VERT")
self.only_I = False
self.only_dIdV = False
self.pointers = []
self.fname = os.getcwdu()
self.plotting = "V"
class GenerateProjectorCalibration(HasTraits):
#width = traits.Int
#height = traits.Int
display_id = traits.String
plot = Instance(Component)
linedraw = Instance(LineSegmentTool)
viewport_id = traits.String('viewport_0')
display_mode = traits.Trait('white on black', 'black on white')
client = traits.Any
blit_compressed_image_proxy = traits.Any
set_display_server_mode_proxy = traits.Any
traits_view = View(
Group(
Item('display_mode'),
Item('viewport_id'),
Item('plot', editor=ComponentEditor(),
show_label=False),
orientation = "vertical"),
resizable=True,
)
def __init__(self,*args,**kwargs):
display_coords_filename = kwargs.pop('display_coords_filename')
super( GenerateProjectorCalibration, self ).__init__(*args,**kwargs)
fd = open(display_coords_filename,mode='r')
data = pickle.load(fd)
fd.close()
self.param_name = 'virtual_display_config_json_string'
self.fqdn = '/virtual_displays/'+self.display_id + '/' + self.viewport_id
self.fqpn = self.fqdn + '/' + self.param_name
self.client = dynamic_reconfigure.client.Client(self.fqdn)
self._update_image()
if 1:
virtual_display_json_str = rospy.get_param(self.fqpn)
this_virtual_display = json.loads( virtual_display_json_str )
if 1:
virtual_display_json_str = rospy.get_param(self.fqpn)
this_virtual_display = json.loads( virtual_display_json_str )
all_points_ok = True
# error check
for (x,y) in this_virtual_display['viewport']:
if (x >= self.width) or (y >= self.height):
all_points_ok = False
break
if all_points_ok:
self.linedraw.points = this_virtual_display['viewport']
# else:
# self.linedraw.points = []
self._update_image()
def _update_image(self):
self._image = np.zeros( (self.height, self.width, 3), dtype=np.uint8)
# draw polygon
if len(self.linedraw.points)>=3:
pts = [ (posint(y,self.height-1),posint(x,self.width-1)) for (x,y) in self.linedraw.points]
mahotas.polygon.fill_polygon(pts, self._image[:,:,0])
self._image[:,:,0] *= 255
self._image[:,:,1] = self._image[:,:,0]
self._image[:,:,2] = self._image[:,:,0]
# draw red horizontal stripes
for i in range(0,self.height,100):
self._image[i:i+10,:,0] = 255
# draw blue vertical stripes
for i in range(0,self.width,100):
self._image[:,i:i+10,2] = 255
if hasattr(self,'_pd'):
self._pd.set_data("imagedata", self._image)
self.send_array()
if len(self.linedraw.points) >= 3:
self.update_ROS_params()
def _plot_default(self):
self._pd = ArrayPlotData()
self._pd.set_data("imagedata", self._image)
plot = Plot(self._pd, default_origin="top left")
plot.x_axis.orientation = "top"
img_plot = plot.img_plot("imagedata")[0]
plot.bgcolor = "white"
# Tweak some of the plot properties
plot.title = "Click to add points, press Enter to clear selection"
plot.padding = 50
plot.line_width = 1
# Attach some tools to the plot
pan = PanTool(plot, drag_button="right", constrain_key="shift")
plot.tools.append(pan)
zoom = ZoomTool(component=plot, tool_mode="box", always_on=False)
plot.overlays.append(zoom)
return plot
def _linedraw_default(self):
linedraw = LineSegmentTool(self.plot,color=(0.5,0.5,0.9,1.0))
self.plot.overlays.append(linedraw)
linedraw.on_trait_change( self.points_changed, 'points[]')
return linedraw
def points_changed(self):
self._update_image()
@traits.on_trait_change('display_mode')
def send_array(self):
# create an array
if self.display_mode.endswith(' on black'):
bgcolor = (0,0,0,1)
elif self.display_mode.endswith(' on white'):
bgcolor = (1,1,1,1)
if self.display_mode.startswith('black '):
color = (0,0,0,1)
elif self.display_mode.startswith('white '):
color = (1,1,1,1)
fname = tempfile.mktemp('.png')
try:
scipy.misc.imsave(fname, self._image )
image = freemovr_engine.msg.FreemoVRCompressedImage()
image.format = 'png'
image.data = open(fname).read()
self.blit_compressed_image_proxy(image)
finally:
os.unlink(fname)
def get_viewport_verts(self):
# convert to integers
pts = [ (posint(x,self.width-1),posint(y,self.height-1)) for (x,y) in self.linedraw.points]
# convert to list of lists for maximal json compatibility
return [ list(x) for x in pts ]
class DeviceAnalogInState(traits.HasTraits):
"""encapsulate all (relevant) analog input state on the device
Making these variables a member of their own HasTraits class means
that updates to the device can be treated in an atomic way.
"""
# Analog input state
AIN0_enabled = traits.Bool(False)
AIN0_name = traits.String("AIN0")
AIN1_enabled = traits.Bool(False)
AIN1_name = traits.String("AIN1")
AIN2_enabled = traits.Bool(True)
AIN2_name = traits.String("AIN2")
AIN3_enabled = traits.Bool(False)
AIN3_name = traits.String("AIN3")
trigger_device = traits.Instance('DeviceModel',transient=True)
adc_prescaler = traits.Trait(128.0,{
128.0:0x07,64.0: 0x06,
# According to Atmel's at90usb1287 manual, faster than this is
# too fast to get good measurements with 8MHz crystal.
## '32': 0x05,'16': 0x04,'8': 0x03,
## '4': 0x02,'2': 0x00, # also 0x01
})
downsample_bits = traits.Range(low=0,high=2**5-1,value=0)
AIN_running = traits.Bool(False)
sample_rate_total = traits.Property(label='Sample rate (Hz), all channels',
depends_on=['adc_prescaler',
'trigger_device',
'downsample_bits'])
sample_rate_chan = traits.Property(label='each channel',
depends_on=['sample_rate_total',
'AIN0_enabled','AIN1_enabled',
'AIN2_enabled','AIN3_enabled',])
# but useful when plotting/saving data
Vcc = traits.Float(3.3)
traits_view = View(Group(Group(Item('AIN_running'),
Item(
'Vcc',
tooltip=('This does not set Vcc on the AT90USBKEY. Use to record the '
'value of Vcc. (default = 3.3V)')),
orientation='horizontal'),
Group(Item('AIN0_enabled',padding=0),
Item('AIN0_name',padding=0),
Item('AIN1_enabled',padding=0),
Item('AIN1_name',padding=0),
padding=0,
orientation='horizontal'),
Group(Item('AIN2_enabled',padding=0),
Item('AIN2_name',padding=0),
Item('AIN3_enabled',padding=0),
Item('AIN3_name',padding=0),
padding=0,
orientation='horizontal'),
Group(Item('adc_prescaler'),
Item('downsample_bits'),
orientation='horizontal'),
Group(Item('sample_rate_total',
#show_label=False,
style='readonly',
),
Item('sample_rate_chan',
#show_label=False,
style='readonly',
),
orientation='horizontal'),
))
@traits.cached_property
def _get_sample_rate_total(self):
if self.trigger_device is not None:
input_frequency = self.trigger_device.FOSC/self.adc_prescaler
else:
input_frequency = 100*1e3 # fake value
# from USBKEY datasheet:
if input_frequency < 50*1e3:
warnings.warn('ADC sample frequency is too slow to get good sampling')
if input_frequency > 200*1e3:
warnings.warn('ADC sample frequency is too fast to get good sampling')
#print 'input_frequency %.1f (kHz)'%(input_frequency/1000.0,)
clock_cycles_per_sample = 13.0
clock_adc = input_frequency/clock_cycles_per_sample
downsample_factor = self.downsample_bits+1
downsampled_clock_adc = clock_adc/downsample_factor
return downsampled_clock_adc
@traits.cached_property
def _get_sample_rate_chan(self):
n_chan = sum(map(int,[self.AIN0_enabled,self.AIN1_enabled,
self.AIN2_enabled,self.AIN3_enabled]))
if n_chan == 0:
return 0.0
rate = self.sample_rate_total/float(n_chan)
return rate
class itkConstantImageMathInputSpec(CommandLineInputSpec):
inFilename = File(argstr='%s', desc = "inFilename", exists = True, mandatory = True, position = 0)
fileMode = traits.Str(argstr='%s', desc = "fileMode", exists = True, mandatory = True, position = 1)
value = traits.Int(argstr='%s', desc = "value", exists = True, mandatory = True, position = 2)
operation = traits.String(argstr='%s', desc = "operation", exists = True, mandatory = True, position = 3)
outFilename = traits.Str(argstr='%s', desc = "outFilename", exists = True, mandatory = True, position = 4)
class Fit(traits.HasTraits):
name = traits.Str(desc="name of fit")
function = traits.Str(desc="function we are fitting with all parameters")
variablesList = traits.List(Parameter)
calculatedParametersList = traits.List(CalculatedParameter)
xs = None # will be a scipy array
ys = None # will be a scipy array
zs = None # will be a scipy array
performFitButton = traits.Button("Perform Fit")
getInitialParametersButton = traits.Button("Guess Initial Values")
usePreviousFitValuesButton = traits.Button("Use Previous Fit")
drawRequestButton = traits.Button("Draw Fit")
setSizeButton = traits.Button("Set Initial Size")
chooseVariablesButtons = traits.Button("choose logged variables")
logLibrarianButton = traits.Button("librarian")
logLastFitButton = traits.Button("log current fit")
removeLastFitButton = traits.Button("remove last fit")
autoFitBool = traits.Bool(
False,
desc=
"Automatically perform this Fit with current settings whenever a new image is loaded"
)
autoGuessBool = traits.Bool(
False,
desc=
"Whenever a fit is completed replace the guess values with the calculated values (useful for increasing speed of the next fit)"
)
autoDrawBool = traits.Bool(
False,
desc=
"Once a fit is complete update the drawing of the fit or draw the fit for the first time"
)
autoSizeBool = traits.Bool(
False,
desc=
"If TOF variable is read from latest XML and is equal to 0.11ms (or time set in Physics) then it will automatically update the physics sizex and sizey with the Sigma x and sigma y from the gaussian fit"
)
logBool = traits.Bool(
False, desc="Log the calculated and fitted values with a timestamp")
logName = traits.String(
desc="name of the scan - will be used in the folder name")
logDirectory = os.path.join("\\\\ursa", "AQOGroupFolder",
"Experiment Humphry", "Data", "eagleLogs")
latestSequence = os.path.join("\\\\ursa", "AQOGroupFolder",
"Experiment Humphry",
"Experiment Control And Software",
"currentSequence", "latestSequence.xml")
logFile = traits.File(desc="file path of logFile")
logAnalyserBool = traits.Bool(
False, desc="only use log analyser script when True")
logAnalysers = [
] #list containing full paths to each logAnalyser file to run
logAnalyserDisplayString = traits.String(
desc=
"comma separated read only string that is a list of all logAnalyser python scripts to run. Use button to choose files"
)
logAnalyserSelectButton = traits.Button("sel. analyser",
image='@icons:function_node',
style="toolbar")
xmlLogVariables = []
imageInspectorReference = None #will be a reference to the image inspector
fitting = traits.Bool(False) #true when performing fit
fitted = traits.Bool(
False) #true when current data displayed has been fitted
fitSubSpace = traits.Bool(
False) #true when current data displayed has been fitted
startX = traits.Int
startY = traits.Int
endX = traits.Int
endY = traits.Int
fittingStatus = traits.Str()
fitThread = None
fitTimeLimit = traits.Float(
10.0,
desc=
"Time limit in seconds for fitting function. Only has an effect when fitTimeLimitBool is True"
)
fitTimeLimitBool = traits.Bool(
True,
desc=
"If True then fitting functions will be limited to time limit defined by fitTimeLimit "
)
physics = traits.Instance(
physicsProperties.physicsProperties.PhysicsProperties)
#status strings
notFittedForCurrentStatus = "Not Fitted for Current Image"
fittedForCurrentImageStatus = "Fit Complete for Current Image"
currentlyFittingStatus = "Currently Fitting..."
failedFitStatus = "Failed to finish fit. See logger"
timeExceededStatus = "Fit exceeded user time limit"
lmfitModel = traits.Instance(
lmfit.Model
) #reference to the lmfit model must be initialised in subclass
mostRecentModelResult = None # updated to the most recent ModelResult object from lmfit when a fit thread is performed
fitSubSpaceGroup = traitsui.VGroup(
traitsui.Item("fitSubSpace", label="Fit Sub Space", resizable=True),
traitsui.VGroup(traitsui.HGroup(
traitsui.Item("startX", resizable=True),
traitsui.Item("startY", resizable=True)),
traitsui.HGroup(traitsui.Item("endX", resizable=True),
traitsui.Item("endY", resizable=True)),
visible_when="fitSubSpace"),
label="Fit Sub Space",
show_border=True)
generalGroup = traitsui.VGroup(traitsui.Item("name",
label="Fit Name",
style="readonly",
resizable=True),
traitsui.Item("function",
label="Fit Function",
style="readonly",
resizable=True),
fitSubSpaceGroup,
label="Fit",
show_border=True)
variablesGroup = traitsui.VGroup(traitsui.Item(
"variablesList",
editor=traitsui.ListEditor(style="custom"),
show_label=False,
resizable=True),
show_border=True,
label="parameters")
derivedGroup = traitsui.VGroup(traitsui.Item(
"calculatedParametersList",
editor=traitsui.ListEditor(style="custom"),
show_label=False,
resizable=True),
show_border=True,
label="derived values")
buttons = traitsui.VGroup(
traitsui.HGroup(
traitsui.Item("autoFitBool", label="Auto fit?", resizable=True),
traitsui.Item("performFitButton", show_label=False,
resizable=True)),
traitsui.HGroup(
traitsui.Item("autoGuessBool", label="Auto guess?",
resizable=True),
traitsui.Item("getInitialParametersButton",
show_label=False,
resizable=True)),
traitsui.HGroup(
traitsui.Item("autoDrawBool", label="Auto draw?", resizable=True),
traitsui.Item("drawRequestButton",
show_label=False,
resizable=True)),
traitsui.HGroup(
traitsui.Item("autoSizeBool", label="Auto size?", resizable=True),
traitsui.Item("setSizeButton", show_label=False, resizable=True)),
traitsui.HGroup(
traitsui.Item("usePreviousFitValuesButton",
show_label=False,
resizable=True)))
logGroup = traitsui.VGroup(traitsui.HGroup(
traitsui.Item("logBool", resizable=True),
traitsui.Item("chooseVariablesButtons",
show_label=False,
resizable=True)),
traitsui.HGroup(
traitsui.Item("logName", resizable=True)),
traitsui.HGroup(
traitsui.Item("removeLastFitButton",
show_label=False,
resizable=True),
traitsui.Item("logLastFitButton",
show_label=False,
resizable=True)),
traitsui.HGroup(
traitsui.Item("logAnalyserBool",
label="analyser?",
resizable=True),
traitsui.Item("logAnalyserDisplayString",
show_label=False,
style="readonly",
resizable=True),
traitsui.Item("logAnalyserSelectButton",
show_label=False,
resizable=True)),
label="Logging",
show_border=True)
actionsGroup = traitsui.VGroup(traitsui.Item("fittingStatus",
style="readonly",
resizable=True),
logGroup,
buttons,
label="Fit Actions",
show_border=True)
traits_view = traitsui.View(traitsui.VGroup(generalGroup, variablesGroup,
derivedGroup, actionsGroup),
kind="subpanel")
def __init__(self, **traitsDict):
super(Fit, self).__init__(**traitsDict)
self.startX = 0
self.startY = 0
self.lmfitModel = lmfit.Model(self.fitFunc)
def _set_xs(self, xs):
self.xs = xs
def _set_ys(self, ys):
self.ys = ys
def _set_zs(self, zs):
self.zs = zs
def _fittingStatus_default(self):
return self.notFittedForCurrentStatus
def _getInitialValues(self):
"""returns ordered list of initial values from variables List """
return [_.initialValue for _ in self.variablesList]
def _getParameters(self):
"""creates an lmfit parameters object based on the user input in variablesList """
return lmfit.Parameters(
{_.name: _.parameter
for _ in self.variablesList})
def _getCalculatedValues(self):
"""returns ordered list of fitted values from variables List """
return [_.calculatedValue for _ in self.variablesList]
def _intelligentInitialValues(self):
"""If possible we can auto set the initial parameters to intelligent guesses user can always overwrite them """
self._setInitialValues(self._getIntelligentInitialValues())
def _get_subSpaceArrays(self):
"""returns the arrays of the selected sub space. If subspace is not
activated then returns the full arrays"""
if self.fitSubSpace:
xs = self.xs[self.startX:self.endX]
ys = self.ys[self.startY:self.endY]
logger.info("xs array sliced length %s " % (xs.shape))
logger.info("ys array sliced length %s " % (ys.shape))
zs = self.zs[self.startY:self.endY, self.startX:self.endX]
logger.info("zs sub space array %s,%s " % (zs.shape))
return xs, ys, zs
else:
return self.xs, self.ys, self.zs
def _getIntelligentInitialValues(self):
"""If possible we can auto set the initial parameters to intelligent guesses user can always overwrite them """
logger.debug("Dummy function should not be called directly")
return
#in python this should be a pass statement. I.e. user has to overwrite this
def fitFunc(self, data, *p):
"""Function that we are trying to fit to. """
logger.error("Dummy function should not be called directly")
return
#in python this should be a pass statement. I.e. user has to overwrite this
def _setCalculatedValues(self, modelFitResult):
"""updates calculated values with calculated argument """
parametersResult = modelFitResult.params
for variable in self.variablesList:
variable.calculatedValue = parametersResult[variable.name].value
def _setCalculatedValuesErrors(self, modelFitResult):
"""given the covariance matrix returned by scipy optimize fit
convert this into stdeviation errors for parameters list and updated
the stdevError attribute of variables"""
parametersResult = modelFitResult.params
for variable in self.variablesList:
variable.stdevError = parametersResult[variable.name].stderr
def _setInitialValues(self, guesses):
"""updates calculated values with calculated argument """
c = 0
for variable in self.variablesList:
variable.initialValue = guesses[c]
c += 1
def deriveCalculatedParameters(self):
"""Wrapper for subclass definition of deriving calculated parameters
can put more general calls in here"""
if self.fitted:
self._deriveCalculatedParameters()
def _deriveCalculatedParameters(self):
"""Should be implemented by subclass. should update all variables in calculate parameters list"""
logger.error("Should only be called by subclass")
return
def _fit_routine(self):
"""This function performs the fit in an appropriate thread and
updates necessary values when the fit has been performed"""
self.fitting = True
if self.fitThread and self.fitThread.isAlive():
logger.warning(
"Fitting is already running. You should wait till this fit has timed out before a new thread is started...."
)
#logger.warning("I will start a new fitting thread but your previous thread may finish at some undetermined time. you probably had bad starting conditions :( !")
return
self.fitThread = FitThread() #new fitting thread
self.fitThread.fitReference = self
self.fitThread.isCurrentFitThread = True # user can create multiple fit threads on a particular fit but only the latest one will have an effect in the GUI
self.fitThread.start()
self.fittingStatus = self.currentlyFittingStatus
def _perform_fit(self):
"""Perform the fit using scipy optimise curve fit.
We must supply x and y as one argument and zs as anothger. in the form
xs: 0 1 2 0 1 2 0
ys: 0 0 0 1 1 1 2
zs: 1 5 6 1 9 8 2
Hence the use of repeat and tile in positions and unravel for zs
initially xs,ys is a linspace array and zs is a 2d image array
"""
if self.xs is None or self.ys is None or self.zs is None:
logger.warning(
"attempted to fit data but had no data inside the Fit object. set xs,ys,zs first"
)
return ([], [])
params = self._getParameters()
if self.fitSubSpace: #fit only the sub space
#create xs, ys and zs which are appropriate slices of the arrays
xs, ys, zs = self._get_subSpaceArrays()
else: #fit the whole array of data (slower)
xs, ys, zs = self.xs, self.ys, self.zs
positions = scipy.array([
scipy.tile(xs, len(ys)),
scipy.repeat(ys, len(xs))
]) #for creating data necessary for gauss2D function
if self.fitTimeLimitBool:
modelFitResult = self.lmfitModel.fit(scipy.ravel(zs),
positions=positions,
params=params,
iter_cb=self.getFitCallback(
time.time()))
else: #no iter callback
modelFitResult = self.lmfitModel.fit(scipy.ravel(zs),
positions=positions,
params=params)
return modelFitResult
def getFitCallback(self, startTime):
"""returns the callback function that is called at every iteration of fit to check if it
has been running too long"""
def fitCallback(params, iter, resid, *args, **kws):
"""check the time and compare to start time """
if time.time() - startTime > self.fitTimeLimit:
raise FitException("Fit time exceeded user limit")
return fitCallback
def _performFitButton_fired(self):
self._fit_routine()
def _getInitialParametersButton_fired(self):
self._intelligentInitialValues()
def _drawRequestButton_fired(self):
"""tells the imageInspector to try and draw this fit as an overlay contour plot"""
self.imageInspectorReference.addFitPlot(self)
def _setSizeButton_fired(self):
"""use the sigmaX and sigmaY from the current fit to overwrite the
inTrapSizeX and inTrapSizeY parameters in the Physics Instance"""
self.physics.inTrapSizeX = abs(self.sigmax.calculatedValue)
self.physics.inTrapSizeY = abs(self.sigmay.calculatedValue)
def _getFitFuncData(self):
"""if data has been fitted, this returns the zs data for the ideal
fitted function using the calculated paramters"""
positions = [
scipy.tile(self.xs, len(self.ys)),
scipy.repeat(self.ys, len(self.xs))
] #for creating data necessary for gauss2D function
zsravelled = self.fitFunc(positions, *self._getCalculatedValues())
return zsravelled.reshape(self.zs.shape)
def _logAnalyserSelectButton_fired(self):
"""open a fast file editor for selecting many files """
fileDialog = FileDialog(action="open files")
fileDialog.open()
if fileDialog.return_code == pyface.constant.OK:
self.logAnalysers = fileDialog.paths
logger.info("selected log analysers: %s " % self.logAnalysers)
self.logAnalyserDisplayString = str(
[os.path.split(path)[1] for path in self.logAnalysers])
def runSingleAnalyser(self, module):
"""runs the logAnalyser module calling the run function and returns the
columnNames and values as a list"""
exec("import logAnalysers.%s as currentAnalyser" % module)
reload(
currentAnalyser
) #in case it has changed..#could make this only when user requests
#now the array also contains the raw image as this may be different to zs if you are using a processor
if hasattr(self.imageInspectorReference, "rawImage"):
rawImage = self.imageInspectorReference.rawImage
else:
rawImage = None
return currentAnalyser.run([self.xs, self.ys, self.zs, rawImage],
self.physics.variables, self.variablesList,
self.calculatedParametersList)
def runAnalyser(self):
""" if logAnalyserBool is true we perform runAnalyser at the end of _log_fit
runAnalyser checks that logAnalyser exists and is a python script with a valid run()function
it then performs the run method and passes to the run function:
-the image data as a numpy array
-the xml variables dictionary
-the fitted paramaters
-the derived values"""
for logAnalyser in self.logAnalysers:
if not os.path.isfile(logAnalyser):
logger.error(
"attempted to runAnalyser but could not find the logAnalyser File: %s"
% logAnalyser)
return
#these will contain the final column names and values
finalColumns = []
finalValues = []
#iterate over each selected logAnalyser get the column names and values and add them to the master lists
for logAnalyser in self.logAnalysers:
directory, module = os.path.split(logAnalyser)
module, ext = os.path.splitext(module)
if ext != ".py":
logger.error("file was not a python module. %s" % logAnalyser)
else:
columns, values = self.runSingleAnalyser(module)
finalColumns.extend(columns)
finalValues.extend(values)
return finalColumns, finalValues
def mostRecentModelFitReport(self):
"""returns the lmfit fit report of the most recent
lmfit model results object"""
if self.mostRecentModelResult is not None:
return lmfit.fit_report(self.mostRecentModelResult) + "\n\n"
else:
return "No fit performed"
def getCalculatedParameters(self):
"""useful for print returns tuple list of calculated parameter name and value """
return [(_.name, _.value) for _ in self.calculatedParametersList]
def _log_fit(self):
if self.logName == "":
logger.warning("no log file defined. Will not log")
return
#generate folders if they don't exist
logFolder = os.path.join(self.logDirectory, self.logName)
if not os.path.isdir(logFolder):
logger.info("creating a new log folder %s" % logFolder)
os.mkdir(logFolder)
imagesFolder = os.path.join(logFolder, "images")
if not os.path.isdir(imagesFolder):
logger.info("creating a new images Folder %s" % imagesFolder)
os.mkdir(imagesFolder)
commentsFile = os.path.join(logFolder, "comments.txt")
if not os.path.exists(commentsFile):
logger.info("creating a comments file %s" % commentsFile)
open(commentsFile,
"a+").close() #create a comments file in every folder!
firstSequenceCopy = os.path.join(logFolder,
"copyOfInitialSequence.ctr")
if not os.path.exists(firstSequenceCopy):
logger.info("creating a copy of the first sequence %s -> %s" %
(self.latestSequence, firstSequenceCopy))
shutil.copy(self.latestSequence, firstSequenceCopy)
if self.imageInspectorReference.model.imageMode == "process raw image": #if we are using a processor, save the details of the processor used to the log folder
processorParamtersFile = os.path.join(logFolder,
"processorOptions.txt")
processorPythonScript = os.path.join(logFolder,
"usedProcessor.py") #TODO!
if not os.path.exists(processorParamtersFile):
with open(processorParamtersFile, "a+") as processorParamsFile:
string = str(self.imageInspectorReference.model.
chosenProcessor) + "\n"
string += str(self.imageInspectorReference.model.processor.
optionsDict)
processorParamsFile.write(string)
logger.debug("finished all checks on log folder")
#copy current image
try:
shutil.copy(self.imageInspectorReference.selectedFile,
imagesFolder)
except IOError as e:
logger.error("Could not copy image. Got IOError: %s " % e.message)
except Exception as e:
logger.error("Could not copy image. Got %s: %s " %
(type(e), e.message))
raise e
logger.info("copying current image")
self.logFile = os.path.join(logFolder, self.logName + ".csv")
#analyser logic
if self.logAnalyserBool: #run the analyser script as requested
logger.info(
"log analyser bool enabled... will attempt to run analyser script"
)
analyserResult = self.runAnalyser()
logger.info("analyser result = %s " % list(analyserResult))
if analyserResult is None:
analyserColumnNames = []
analyserValues = []
#analyser failed. continue as if nothing happened
else:
analyserColumnNames, analyserValues = analyserResult
else: #no analyser enabled
analyserColumnNames = []
analyserValues = []
if not os.path.exists(self.logFile):
variables = [_.name for _ in self.variablesList]
calculated = [_.name for _ in self.calculatedParametersList]
times = ["datetime", "epoch seconds"]
info = ["img file name"]
xmlVariables = self.xmlLogVariables
columnNames = times + info + variables + calculated + xmlVariables + analyserColumnNames
with open(
self.logFile, 'ab+'
) as logFile: # note use of binary file so that windows doesn't write too many /r
writer = csv.writer(logFile)
writer.writerow(columnNames)
#column names already exist so...
logger.debug("copying current image")
variables = [_.calculatedValue for _ in self.variablesList]
calculated = [_.value for _ in self.calculatedParametersList]
now = time.time() #epoch seconds
timeTuple = time.localtime(now)
date = time.strftime("%Y-%m-%dT%H:%M:%S", timeTuple)
times = [date, now]
info = [self.imageInspectorReference.selectedFile]
xmlVariables = [
self.physics.variables[varName] for varName in self.xmlLogVariables
]
data = times + info + variables + calculated + xmlVariables + analyserValues
with open(self.logFile, 'ab+') as logFile:
writer = csv.writer(logFile)
writer.writerow(data)
def _logLastFitButton_fired(self):
"""logs the fit. User can use this for non automated logging. i.e. log
particular fits"""
self._log_fit()
def _removeLastFitButton_fired(self):
"""removes the last line in the log file """
logFolder = os.path.join(self.logDirectory, self.logName)
self.logFile = os.path.join(logFolder, self.logName + ".csv")
if self.logFile == "":
logger.warning("no log file defined. Will not log")
return
if not os.path.exists(self.logFile):
logger.error(
"cant remove a line from a log file that doesn't exist")
with open(self.logFile, 'r') as logFile:
lines = logFile.readlines()
with open(self.logFile, 'wb') as logFile:
logFile.writelines(lines[:-1])
def saveLastFit(self):
"""saves result of last fit to a txt/csv file. This can be useful for live analysis
or for generating sequences based on result of last fit"""
try:
with open(
self.imageInspectorReference.cameraModel + "-" +
self.physics.species + "-" + "lastFit.csv",
"wb") as lastFitFile:
writer = csv.writer(lastFitFile)
writer.writerow(["time", time.time()])
for variable in self.variablesList:
writer.writerow([variable.name, variable.calculatedValue])
for variable in self.calculatedParametersList:
writer.writerow([variable.name, variable.value])
except Exception as e:
logger.error("failed to save last fit to text file. message %s " %
e.message)
def _chooseVariablesButtons_fired(self):
self.xmlLogVariables = self.chooseVariables()
def _usePreviousFitValuesButton_fired(self):
"""update the guess initial values with the value from the last fit """
logger.info(
"use previous fit values button fired. loading previous initial values"
)
self._setInitialValues(self._getCalculatedValues())
def chooseVariables(self):
"""Opens a dialog asking user to select columns from a data File that has
been selected. THese are then returned as a string suitable for Y cols input"""
columns = self.physics.variables.keys()
columns.sort()
values = zip(range(0, len(columns)), columns)
checklist_group = traitsui.Group(
'10', # insert vertical space
traitsui.Label('Select the additional variables you wish to log'),
traitsui.UItem('columns',
style='custom',
editor=traitsui.CheckListEditor(values=values,
cols=6)),
traitsui.UItem('selectAllButton'))
traits_view = traitsui.View(checklist_group,
title='CheckListEditor',
buttons=['OK'],
resizable=True,
kind='livemodal')
col = ColumnEditor(numberOfColumns=len(columns))
try:
col.columns = [
columns.index(varName) for varName in self.xmlLogVariables
]
except Exception as e:
logger.error(
"couldn't selected correct variable names. Returning empty selection"
)
logger.error("%s " % e.message)
col.columns = []
col.edit_traits(view=traits_view)
logger.debug("value of columns selected = %s ", col.columns)
logger.debug("value of columns selected = %s ",
[columns[i] for i in col.columns])
return [columns[i] for i in col.columns]
def _logLibrarianButton_fired(self):
"""opens log librarian for current folder in logName box. """
logFolder = os.path.join(self.logDirectory, self.logName)
if not os.path.isdir(logFolder):
logger.error(
"cant open librarian on a log that doesn't exist.... Could not find %s"
% logFolder)
return
librarian = plotObjects.logLibrarian.Librarian(logFolder=logFolder)
librarian.edit_traits()