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Parsing of input parameters

Parsing "on knees"

import sys
import os

def get_input_parameters() :
    nargs = len(sys.argv)
    print 'sys.argv[0]: ', sys.argv[0]
    print 'nargs: ', nargs
    # Then do something with arguments...

Use OptionParser

from optparse import OptionParser

def input_option_parser() :

    def_fname = 'spec-xppi0412-r0060-20120507-125420.198726277.txt'
    def_cols = 100

    parser = OptionParser(description='Process optional input parameters.', usage = "usage: %prog [options]")
    parser.add_option('-f', '--fname', dest='fname', default=def_fname, action='store', type='string', help='input file name')
    parser.add_option('-c', '--cols', dest='cols', default=def_cols, action='store', type='int', help='number of columns in the image array')
    parser.add_option('-v', dest='verbose', action='store_true',  help='set flag to print more details',  default=True)
    parser.add_option('-q', dest='verbose', action='store_false', help='set flag to print less details')
    (opts, args) = parser.parse_args()

    print 'opts:',opts
    print 'args:',args

    return (opts, args)

Manipulation with directories and files

Access to files in the derectory

def getListOfFilesInDir(dirname) :
    return os.listdir(dirname)

def printListOfFilesInDir(dirname) :
    print 'List of files in the dir.', dirname
    for name in os.listdir(dirname) :
        print name
    print '\n'

Parsing the pathname

        root, ext = os.path.splitext(path) # i.e. path='root-part.tail-part'
        basename  = os.path.basename(path)
        dirname   = os.path.dirname(path)
        lexist    = os.path.lexists(path)
        isfile    = os.path.isfile(path)
        isdir     = os.path.isdir(path)
        head, tail= os.path.split(path)    # i.e. path='head-part/tail-part'
...

http://docs.python.org/library/os.path.html

Joint path and name

        path_name = os.path.join(path,fname)

Useful string parsing options

http://docs.python.org/library/string.html

    string.rsplit(str, sep, maxsplit)
    string.capitalize(word)
    string.lower(s)
    start = string.find(symbolic_string, pattern)
    pattern_length = len(pattern)

http://docs.python.org/library/parser.html?

Or use more shorter methods for str object:
http://docs.python.org/library/stdtypes.html, for example:

    par_str = line[pos_eq+1:].strip(' ').rstrip('\n')

Replace the part of the string

 my_string.replace("abcde","cde")

Python - useful references

Built-in functions

http://docs.python.org/library/functions.html

setattr - gives dynamic variables in python

http://docs.python.org/library/functions.html#setattr

PyQt4

PyQt4 class references

All classes
Selected:

Open/close/move other GUI window

Try to close window if its object exists, othervise - open:

    def processConfigPars(self):
        print 'processConfigPars'
        try :
            cp.confpars.guiconfigparameters.close()
        except : # AttributeError: #NameError 
            cp.confpars.guiconfigparameters = guiconfigpars.GUIConfigParameters()
            cp.confpars.guiconfigparameters.move(self.pos().__add__(QtCore.QPoint(100,330))) # window offset
            # or use self.parentWidget().pos() for combined widgets:
            # cp.guifilebrowser.move(self.parentWidget().pos().__add__(QtCore.QPoint(240,40)))
            cp.confpars.guiconfigparameters.show()

Sometime it looks like the window does not want to move in specified position...
In particular I have observed, that everything is going correct untill the w.show(). then, suddenly happens moveEvent(), which changes the self.pos(). In my case it happened because at construction of the combined window, its size was changed and it was moved in origin... Reservation of larger window size solved this problem.

Close window and delete object

    def closeEvent(self, event):
        try: # try to delete self object in the cp.confpars
            del cp.confpars.guiconfigparameters 
        except # AttributeError:
            pass # silently ignore

Change style of buttons depending on status

For particular QPushButton it works: 

self.but_path = QtGui.QPushButton('File:')
self.but_path.setObjectName('but_path')
self.but_path.setStyleSheet('QPushButton#but_path:pressed  {color: black; background-color: green;}' +
                            'QPushButton#but_path:disabled {color: white; background-color: pink;}' +
                            'QPushButton                   {color:  blue; background-color: yellow;}')

For entire application it should be like:

app = QtGui.QApplication.instance()
app.setStyleSheet('QLabel{color: #fff;} QPushButton{background-color: #000; color: #fff}')

but does not work for me...

Make window visible on the top

 widg.raise_()

Scroll down text in

Assuming

 self.box_txt = QtGui.QTextEdit()
 self.box_txt.setText('some text')
 self.box_txt.append('a lot of additional text, exceeding the window size')
 self.box_txt.ensureCursorVisible()

Scroll bar can be used, but result is not seen imidiately:

  scrol_bar_v = self.box_txt.verticalScrollBar() # QScrollBar
  scrol_bar_v.setValue(scrol_bar_v.maximum())

Moving text cursor with repaint() works immidiately:

  self.box_txt.moveCursor(QtGui.QTextCursor.End)
  self.box_txt.repaint()

Set optimal table-widget size

    self.table = QtGui.QTableWidget(rows, cols, self)
    ...
    self.table.setFixedWidth(self.table.horizontalHeader().length() + 4)
    self.table.setFixedHeight(self.table.verticalHeader().length() + 29)

Show image in QLabel

Assumes:

class GUIImage ( QtGui.QLabel ) :
    def __init__ (self, parent=None, app=None) :

        QtGui.QLabel.__init__(self, parent)

        self.setGeometry(200, 100, 100, 100)
        self.setWindowTitle('Image For Grabber')

        self.setFrame()
        ...

i.e. self is an instance of QLabel.

Set pixmap for image

    def setPixmapForImage(self):
        if self.r_pixmap == None :
            self.s_pixmap = None
            self.clear()
        else :
            self.s_pixmap = self.r_pixmap.scaled(self.size(), QtCore.Qt.KeepAspectRatio)
            self.setPixmap(self.s_pixmap)
            self.setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignLeft)
            self.setScailedMask()

Grab image from monitor

    def grabImage(self):
        fname = tempfile.NamedTemporaryFile(mode='r+b',suffix='.ppm')
        if( 0 == os.system('import -trim -frame -border %s' % (fname.name))) :
            self.r_pixmap = QtGui.QPixmap(QtGui.QImage(fname.name)) 
            self.setPixmapForImage()

Grab entire monitor window

    def grabEntireWindow(self):
        self.r_pixmap = QtGui.QPixmap.grabWindow(QtGui.QApplication.desktop().winId())
        self.setPixmapForImage()

Load image from file

   def loadImageFromFile(self, fname) : 
        #Read formats: bmp, jpg, jpeg, png, ppm, xbm, xpm + gif, pbm, pgm, 
        self.r_pixmap = QtGui.QPixmap(QtGui.QImage(fname))     
        self.setPixmapForImage()

Set the mask to suppress the background layer

    def setScailedMask(self):
        size = self.s_pixmap.size()
        print 'Scaled pixmap size: %d x %d' % (size.width(), size.height())
        #==================================
        self.qimage_mask = QtGui.QImage(size, QtGui.QImage.Format_Mono)
        self.qimage_mask.fill(0)
        self.qbitmap_mask = QtGui.QBitmap.fromImage(self.qimage_mask)
        self.s_pixmap.setMask(self.qbitmap_mask)
        #==================================

Save image in file

    def saveImageInFile(self, fname='test.png'): 
        #Write formats: bmp, jpg, jpeg, png, pbm, pgm, ppm, xbm, xpm
        if self.r_pixmap is not None :
            self.r_pixmap.save(fname, format=None)

Set transparent frame

    def setFrame(self):
        self.frame = QtGui.QFrame(self)
        self.frame.setFrameStyle( QtGui.QFrame.Box | QtGui.QFrame.Sunken ) #Box, Panel | Sunken, Raised 
        self.frame.setLineWidth(0)
        self.frame.setMidLineWidth(1)
        self.frame.setGeometry(self.rect())
        #self.frame.setVisible(False)
        self.frame.setStyleSheet('background: transparent;')

Resize event

    def resizeEvent(self, e):
        s = self.size()
        self.frame.setGeometry(QtCore.QRect(0,0,s.width(),s.height()))
        self.setPixmapForImage()

Show image in QtGui.QGraphicsView

QGraphicsView is a class with scrolled graph window...

Graphics in PyQt4

...
        self.poi1  = QtCore.QPoint(0,0)
        self.poi2  = QtCore.QPoint(0,0)
        self.rect1 = QtCore.QRect()
        self.rect2 = QtCore.QRect()

        self.pen1 = QtGui.QPen(QtCore.Qt.black) 
        self.pen2 = QtGui.QPen(QtCore.Qt.white) 
        self.pen1.setStyle(QtCore.Qt.DashLine) 
        self.pen2.setStyle(QtCore.Qt.DashLine) 
        self.pen1.setWidthF(1) 
        self.pen2.setWidthF(1)
...

     def paintEvent(self, e):
        super(GUIImage,self).paintEvent(e)
        qp = QtGui.QPainter()
        # or QPainter can be defined earlier and use it as   qp = self.qp
        qp.begin(self)
        #self.drawPixmap(qp)
        self.drawRect(qp)
        qp.end()
        self.update()

    def setPen(self, qp):
        self.pen.setStyle(QtCore.Qt.DashLine) 
        self.pen.setWidthF(1) 

    def drawRect(self, qp):
        if self.r_pixmap == None:
            return

        p1x, p1y = self.poi1.x(), self.poi1.y()
        p2x, p2y = self.poi2.x(), self.poi2.y()

        R=1
        if abs(p2x-p1x) < R : return
        if abs(p2y-p1y) < R : return

        self.rect1.setCoords( p1x,   p1y,   p2x,   p2y)
        self.rect2.setCoords( p1x+1, p1y+1, p2x-1, p2y-1)
        qp.setPen  (self.pen1)
        qp.drawRect(self.rect1);
        qp.setPen  (self.pen2)
        qp.drawRect(self.rect2);


    def drawPixmap(self, qp):
        if self.r_pixmap != None:
            qp.drawPixmap(0,0,self.s_pixmap)

See other draw options in QPainter class reference.

Style options

    self.styleTransp = "background-color: rgb(255,   0,   0, 100);"
    self.styleTitle  = "background-color: rgb(239, 235, 231, 255); color: rgb(100, 160, 100);" # Gray bkgd
    self.styleWhite  = "background-color: rgb(255, 255, 255); color: rgb(0, 0, 0);" 
    self.styleTitleBold = self.styleTitle + 'font-size: 18pt; font-family: Courier; font-weight: bold;'
    self.styleWhiteFixed= self.styleWhite + 'font-family: Fixed;'

    self.colorEditInfo = QtGui.QColor(100, 255, 200)
    self.colorEditBad  = QtGui.QColor(255,   0,   0)
    self.colorEdit     = QtGui.QColor('white') 

    self.but_close .setStyleSheet (cp.styleButton)
    self.but_close .setFlat(True)
    self.but_logger.setVisible(True) 
    self.box_txt   .setReadOnly(True)
    self.tit_title .setAlignment(QtCore.Qt.AlignTop | QtCore.Qt.AlignCenter)
    self.but_logger.setIcon(cp.icon_contents)

    self.setMinimumWidth(400)
    self.setMinimumHeight(320)
    self.setMinimumSize(600,700)
    self.setFixedHeight(350)

Icons

     path = './icons/'
     self.icon_contents = QtGui.QIcon(path + 'contents.png')
     self.but_logger.setIcon(cp.icon_contents)

Tooltips

        self.edi_usr.setToolTip('Sender of the message')

Matplotlib

In examples below we assume

fig = plt.figure(num=1, figsize=(10,10), dpi=100, facecolor='w',edgecolor='w',frameon=True)
axes = fig.add_subplot(111)
axim = axes.imshow(arrwin, interpolation='nearest', origin='bottom', aspect='auto', extent=[xmin, xmax, ymax, ymin])

Save figure in file

fig.savefig(fname, dpi=240)

Clear figure

fig.clear()

Graphic

axes.plot(xarr1, yarr1, '-r', xarr2, yarr2,  '-g')

Histogram

axes.hist(arr, bins=100, range=(10,50), log=False) # log for vertical scale only

Image (with colorbar)

img = axes.imshow(arr2d, interpolation='nearest', origin='bottom', aspect='auto')
img.set_clim(Amin,Amax)

cbar = self.fig.colorbar(img, orientation='vertical', \
                         fraction=0.1, pad=0.01, shrink=1.0, aspect=20)

        # fraction - of the 2d plot occupied by the color bar
        # pad      - is a space between 2d image and color bar
        # shrink   - factor for the length of the color bar
        # aspect   - ratio length/width of the color bar

Color bar as a separate sub-plot

axcb = fig.add_axes([0.1,  0.1, 0.8, 0.1]) # x0, y0, width, height
cbar = fig.colorbar(img, cax=axcb, orientation='horizontal', \
                    fraction=0.1, pad=0.01, shrink=1.0, aspect=20)
axcb.xaxis.set_ticks_position('top') # change position of axis labels

Define subplot(s) with empty axes

axes  = fig.add_subplot(111)

or

axes1  = fig.add_subplot(211)        
axes2  = fig.add_subplot(212)

Make figure with non-equal subplots

                    # x0, y0, width, height
axgr = fig.add_axes([0.1,  0.64, 0.80, 0.35])
axhi = fig.add_axes([0.1,  0.14, 0.35, 0.35])
axti = fig.add_axes([0.55, 0.14, 0.35, 0.35])

or using grid:

import matplotlib.gridspec as gridspec
gs   = gridspec.GridSpec(20, 20)
# Naive direction        [  Y   ,   X ]
axsa = fig.add_subplot(gs[ 1:16,  0:14])
axsb = fig.add_subplot(gs[ 1:16, 14:19])
axsc = fig.add_subplot(gs[16:  ,  0:14])

Set axes limits

    
axes.set_xlim((-50,50))
axes.set_ylim((-10,210))

Draw line

import matplotlib.lines  as lines
line = lines.Line2D(arrx, arry, linewidth=1, color='r')   
axes.add_artist(line)

Set a number of ticks along the axis

from matplotlib.ticker import MaxNLocator
axes.xaxis.set_major_locator(MaxNLocator(4))

Axis without tick-labels

import matplotlib.ticker as mtick
axes.xaxis.set_major_formatter( mtick.NullFormatter() )

Rotate axis tick-labels

for label in axes.get_xticklabels() :
    label.set_rotation(60)                  # rotate by 60 degree
    label.set_horizontalalignment('center') # 'right', etc.

Change axis tick-label position on the plot

axes.xaxis.set_ticks_position('top')
axes.yaxis.set_ticks_position('right')

Change axis tick-label font size

axes.tick_params(axis='both', which='major', labelsize=8)

Axes labels and size

axes.set_xlabel('Time index', fontsize=10)
axes.set_ylabel('dt(sec)', fontsize=8)

Axes labels with LaTeX symbols

Use raw string with LaTeX notations inside:

axes.set_xlabel(r'$\rho A_i$')

Text in axes

plt.text(x, y, text, fontsize=7, color='k', ha='left', rotation=45)
axes.text(x, y, text, fontsize=7, color='k', ha='left', rotation=45)

Window title for figure

    fig  = plt.figure(figsize=(15,5), dpi=80, facecolor='w',edgecolor='w',frameon=True)
    fig.canvas.set_window_title('Image And Spectrum ' + u'\u03C6')

Axes title

    
plt.title('Image',color='b',fontsize=20)
or
axes.set_title('Image',color='b',fontsize=20)

Log scale methods

Log values:

    
from math import log10
log_vmin, log_vmax = log10(vmin), log10(vmax)

Log scale axes:

axes.set_xscale('log')
axes.set_yscale('log')

Log scale image data:

self.arr2d = np.log10(self.arrwin)
self.imsh = axis.imshow(self.arr2d, origin='upper', \
                                          interpolation='nearest', \
                                          extent=self.range, aspect='auto')
self.imsh.set_clim(log_vmin,log_vmax)

Histogram with log statistics (y axis):

axes.hist(self.arrwin.flatten(), bins=self.nbins, range=self.range_his, log=True)

Plot histogram with log bin size:

logbins=10**np.linspace(log_vmin, log_vmax, nbins)
# or:
logbins=np.logspace(log_vmin, log_vmax, nbins)
self.axhi.hist(self.arrwin.flatten(), bins=logbins )

Window title

    
    fig.canvas.set_window_title('Image And Spectrum ' + u'\u03C6')

Add unicode symbols in string

    
    str = 'Symbol phi: ' + u'\u03C6'

Get canvas and connect it with mouse buttons

canvas = fig.canvas
canvas.mpl_connect('button_press_event',   self.processMouseButtonPress) 
canvas.mpl_connect('button_release_event', self.processMouseButtonRelease) 
canvas.mpl_connect('motion_notify_event',  self.processMouseMotion)

...

    def processMouseButtonPress(self, event) :
        print 'MouseButtonPress'
        print 'event: xdata, ydata, x, y =', event.xdata, event.ydata, event.x, event.y

        if event.inaxes == self.axgr : self.mousePressOnGraph(event)
        if event.inaxes == self.axti : self.mousePressOnGraph(event)
        if event.inaxes == self.axhi : self.mousePressOnHisto(event)

        if event.button == 1 : # 1=left, 2=middle, 3=right
            self.gr_xmin = float(event.xdata)

At the edge of matplotlib and PyQt4

We assume that everything is done in our backend basis:

import matplotlib
matplotlib.use('Qt4Agg')
import matplotlib.pyplot as plt

Check and set backend 

import matplotlib
if matplotlib.get_backend() != 'Qt4Agg' : 
    matplotlib.use('Qt4Agg')

Get the current matplotlib figure window position on monitor

pos = fig.canvas.manager.window.pos()
print 'x,y=', pos.x(), pos.y()

Move the matplotlib figure window in certain (x,y) position

fig.canvas.manager.window.move(x,y) # in pixels from top-left corner

or

plt.get_current_fig_manager().window.move(90, 100)

For our backend starting from python 2.7.2:

plt.get_current_fig_manager().window.geometry("+100+300")

Move the matplotlib figure window on top (of all pileup windows)

fig.canvas.manager.window.activateWindow() # Makes window active
fig.canvas.manager.window.raise_()         # Moves window on top

the attribute trick is that the fig.canvas.manager.window returns the QtGui.QMainWindow, which is subclass of QtGui.QWidget with all that useful methods.

Add figure as a widget of the QtGui

fig = plt.figure(num=None figsize=(5,10), dpi=100, facecolor='w',edgecolor='w',frameon=True)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(fig.canvas)    # Wraps figure canvas in widget 
self.setLayout(vbox)

How to recieve a signal in program when window is activated by the mouse click on frame ?

I do not know yet...

But, if you click on figure canvas (the region inside the window frame, use

        fig.canvas.mpl_connect('button_press_event', self.onButtonPressEvent) 

#Should be implemented something like:
    def onButtonPressEvent( self, event ):
        """Figure is picked"""
        print 'click on fig number =', event.canvas.figure.number

Receive a signal in program when close window by the click on "X"

        fig.canvas.mpl_connect('close_event', self.onCloseEvent)

#Should be implemented something like:
    def onCloseEvent( self, event ):
        print 'close event, fig number =', event.canvas.figure.number

Close figure from program call

plt.close( num ) # close figure with known number num
...
plt.close('all') # close all figures

Emit your own signal in PyQt4

from PyQt4 import QtGui, QtCore
class Drag ( QtCore.QObject ):
    def __init__(self) :
        QtCore.QObject.__init__(self, None) # need it for signal exchange...
    ...

        self.emit( QtCore.SIGNAL('new_xy_center(int,int)'), x, y)

Receive your own signal in PyQt4

from PyQt4 import QtGui, QtCore 
class BatchJobCorAna( QtCore.QObject ) : 
    def __init__(self) :
        QtCore.QObject.__init__(self, None) # need it for signal exchange...
    ...

    def connectToThread1(self):
        #try : self.connect( thread1, QtCore.SIGNAL('update(QString)'), self.updateStatus )
        try : self.connect( thread1, QtCore.SIGNAL('new_xy_center(int,int)'), self.updateStatus )
        except : logger.warning('connectToThread1 IS FAILED !!!', __name__)

    def updateStatus(self, x, y):
        print 'BatchJobCorAna: Signal is recieved, x,y=', x, y

where thread1 is an object emiting the signal.

NumPy

Import

#!/usr/bin/env python
  import numpy as np

Read numpy array from text file

    nparr = np.loadtxt('arr.txt', dtype=np.float)

errors = 0.5*np.random.normal(size=len(yn))

SciPy

Import

#!/usr/bin/env python
import numpy as np
from scipy.optimize import curve_fit

Fit to data

Reference to scipy.optimize.curve_fit
Fitting data example

Working example:

#!/usr/bin/env python
import numpy as np
from scipy.optimize import curve_fit

def func(x, a, b, c):
    return a*np.exp(-b*x) + c

p0 = [2.5, 1.3, 0.5]
x = np.linspace(0, 5, 50)
y = func(x, *p0)

yn = y + 0.2*np.random.normal(size=len(x))
en = 1.1*np.random.normal(size=len(x))

popt, pcov = curve_fit(func, x, yn, p0, en)

yf = func(x, *popt)

print "p0   = ", p0
print "popt = ", popt
print "pcov:\n", pcov

# Let's plot it now
import matplotlib.pyplot as plt

plt.plot( #x, y,  'r-', \
           x, yn, 'g^', \
           x, yf, 'bs-')
plt.show()
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