Content

Table of Contents

Python tricks

Parsing of input parameters

Parsing "on knees"

Code Block
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

Code Block


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

...

Dictionaris, Lists, etc

Make dictionary from two lists

Code Block
k = ['a', 'b', 'c'] v = [1, 2, 3] d = dict(zip(keys, values)) >>> print dictionary {'a': 1, 'b': 2, 'c': 3}

Sorted list

Get sorted list from non-sorted:

Code Block
lst_sorted = sorted(lst)

Define non-default order of elements:

Code Block

    def __cmp__(self, other
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"""Method for sorted()"""
    print '\n'

Parsing the pathname

Code Block


   if self.begin    root, ext = os.path.splitext(path) # i.e. path='root-part.tail-part'< other.begin : return -1
        basenameif self.begin  => os.path.basename(path)
    other.begin : return  1
    dirname    if self.begin == os.path.dirname(path)other.begin : 
        lexist    =if os.path.lexists(path)
        isfileself.end  < other.end : return  1 # inverse comparison for end
     = os.path.isfile(path)
      if self.end isdir > other.end : return = os.path.isdir(path)-1 
        head,   tail= os.path.split(path)    # i.e. path='head-part/tail-part'
...

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

Useful string parsing options

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

if self.end == other.end : return  0

Exceptions

Standard exceptions

Raise exceprion

Code Block
if not os.path.lexists(fname) : raise IOError('File %s is not available' % fname)

Catch exception

Code Block

    try :
        plf = PeakListFile(fname

Code Block


    string.rsplit(str, sep, maxsplit)
    string.capitalize(word)
    string.lower(s)
    startexcept = string.find(symbolic_string, pattern)
Exception as e:
     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:

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

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

How to open/close/move other GUI window?

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

  print 'We cought exception: %s' % e

User defined exception

Code Block

class MyError(Exception):
    def __init__(self, value):
        self.value = value
    def __str__(self):
        return repr(self.value)
...
try:
    raise MyError(2*2)
except MyError as e:
    print 'My exception occurred, value:', e.value

Manipulation with directories and files

Access to files in the derectory

Code Block

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

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

Code Block


    def processConfigPars(self):
        print 'processConfigPars'
        try :
            cp.confpars.guiconfigparameters.close()
        except : # AttributeError: #NameError 
            cp.confpars.guiconfigparameters = guiconfigpars.GUIConfigParameters()
        print name
   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()

Note

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.

How to close window and delete object?

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

Matplotlib

In examples below we assume

Code Block


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')

How to draw histogram

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

How to draw graphic

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

How to define subplot with empty axes

Code Block
axes = fig.add_subplot(111) axes.set_xlim((-50,1750)) axes.set_ylim((-50,1750))

How to make figure with non-equal subplots

Code Block


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])

or even simpler:

Code Block
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])

How to draw line

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

How to draw axis without labels

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

How to rotate axis labels

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

How to set a number of ticks along the axis

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

How to change axis label position on the plot

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

How to draw a color bar as a separate sub-plot

Code Block
axCB = fig.add_subplot(gs[ 0, 0:14]) colb = fig.colorbar(axim, cax=axCB, orientation='horizontal') axCB.xaxis.set_ticks_position('top') # change position of axis labels

How draw text

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

At the edge of matplotlib and PyQt4

We assume that everything is done in our backend basis:

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

How to get the current matplotlib figure window position on monitor

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

How to move the matplotlib figure window in certain (x,y) position

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

How to move the matplotlib figure window on top (of all pileup windows)

Code Block
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.

How to add figure as a widget of the QtGui

Code Block
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 receive 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

Code Block


        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

How to receive a signal in program when close window by the click on "X"

Code Block
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

How to close figure from program call

 print '\n'

Parsing the pathname

Code Block

path = '/reg/d/psdm/cxi/cxif5315/calib/pnccd/pnccd-123456.data'

root, ext = os.path.splitext(path) # ('/reg/d/psdm/cxi/cxif5315/calib/pnccd/pnccd-123456', '.data') # or '' if something is missing
basename  = os.path.basename(path) # pnccd-123456.data 
dirname   = os.path.dirname(path)  # /reg/d/psdm/cxi/cxif5315/calib/pnccd
lexist    = os.path.lexists(path)  # False
isfile    = os.path.isfile(path)   # False
isdir     = os.path.isdir(path)    # False
head, tail= os.path.split(path)    # ('/reg/d/psdm/cxi/cxif5315/calib/pnccd', 'pnccd-123456.data') # or '' if something is missing
...

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

Join list of strings

Code Block
s = ' '.join(sys.argv)

Join path and name

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

Check if string contains pattern

Code Block
exp = 'xpptut13' if 'tut' is in exp : <do something>

String alignment

Code Block
msg = '%s' % (k.ljust(16))

Useful string parsing options

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

Code Block
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:

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

Replace the part of the string

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

String formatting

Code Block
s = 'some text %s %s' % (msg.ljust(30), str(val).rjust(30)

Class string properties

Code Block

    print 'string properties:'
    print 'punctuation    :  ', string.punctuation
    print 'digits         :  ', string.digits
    print 'octdigits      :  ', string.octdigits
    print 'hexdigits      :  ', string.hexdigits
    print 'ascii_letters  :  ', string.ascii_letters
    print 'ascii_lowercase:  ', string.ascii_lowercase
    print 'ascii_uppercase:  ', string.ascii_uppercase
    print 'lowercase      :  ', string.lowercase
    print 'uppercase      :  ', string.uppercase
    print 'letters        :  ', string.letters
    print 'printable      :  ', string.printable
    print 'whitespace     :  ', string.whitespace

Class name

Code Block
self.__class__.__name__

Function name

Code Block
sys._getframe().f_code.co_name

Function parameters

Code Block
locals() # returns (dict) of method input parameters

Converting integer to bin(), oct(), hex() string

using built-in functions

Code Block
ival = 123456 str_bin = bin(ival) str_oct = oct(ival) str_hex = hex(ival)

Time stamp

Code Block

from time import localtime, gmtime, strftime, clock, time

time_sec = time() # epoch time

def get_current_local_time_stamp(fmt='%Y-%m-%d %H:%M:%S %Z'):
    return strftime(fmt, localtime())

def get_current_gm_time_stamp(fmt='%Y-%m-%d %H:%M:%S %Z'):
    return strftime(fmt, gmtime())

def get_local_time_str(time_sec, fmt='%Y-%m-%d %H:%M:%S %Z'):
    return strftime(fmt, localtime(time_sec))

def get_gm_time_str(time_sec, fmt='%Y-%m-%d %H:%M:%S %Z'):
    return strftime(fmt, gmtime(time_sec))

Set PYTHONPATH

In command-line:

Code Block
setenv PYTHONPATH /reg/neh/home1/dubrovin/LCLS/git-work/pyapps:${PYTHONPATH}

In cshell script:

Code Block
alias setpp 'setenv PYTHONPATH /reg/neh/home1/dubrovin/LCLS/git-work/pyapps:${PYTHONPATH}'

In code:

Code Block
import os os.environ['PYTHONPATH'] = '/reg/neh/home1/dubrovin/LCLS/git-work/pyapps:%s' % os.environ.get('PYTHONPATH', '')

Replace symbols in string

Code Block
text.replace("\|",":").replace("-",".") range.replace('9999','end') msg.replace('\n',' ')

List of comprehension

list_of_x2 = [x*x for x in list_of_x]

list_of_x_selected = [x for x,y in zip(list_of_x, list_of_y) if y>0]

map - built-in method

Code Block
def f(x,y) : return x if y>0 else -x list = map(f, arrX, arrY)

Constructor, destructor etc.

Code Block

class PeakListFile :
    def __init__(self, fname) :
	    print 'constructor'
        self.f=open(fname,'r')

    def __del__(self) :
	    print 'destructor'
        try :
            self.f.close()

    def __call__(self) :
	    print 'this is a default method of this object called as obj()'

Polymorphism

Derived class initialization

Code Block
class Base : def __init__(self) : ... class Derived(Base) : def __init__(self) : Base.__init__(self) # OR super(Derived, self).__init__()

Create/save temporary file

Code Block
import tempfile tmp_file = tempfile.NamedTemporaryFile(mode='r+b',suffix='.tiff') tfile = tmp_file.name

Good example of main

Code Block

import sys

def test_all() :
    print _sep_, '\n%s' % sys._getframe().f_code.co_name
    test_ricker()
    test_morlet()

#------------------------------
if __name__ == "__main__" :
    from time import time
    tname = sys.argv[1] if len(sys.argv) > 1 else '0'
    print 50*'_', '\nTest %s:' % tname
    t0_sec = time()
    if   tname == '0': test_all() 
    elif tname == '1': test_ricker()
    elif tname == '2': test_morlet()
    else : print 'Not-recognized test name: %s' % tname
    msg = 'End of test %s, consumed time (sec) = %.6f' % (tname, time()-t0_sec)
    sys.exit(msg)

Virtualenv

Code Block
virtualenv dir-name source <directoryName>/bin/activate.csh # for tcsh # or source <directoryName>/bin/activate # for bash pip install <packageName> ... work deactivate

Python - useful references

Built-in functions

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

setattr, getattr - set/get dynamic variables in python

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

PyQt4

Know How

QGraphicsScene item priority is set by setZValue(v)
All re-implemented Event methods like {{mouseMoveEvent(self, e)}} etc. in items will get control only if QGraphicsView their default version will be called.

PyQt4 class references

All classes
Selected:

Open/close/move other GUI window

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

Code Block

    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()

Note

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

Code Block
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:

Code Block

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:

Code Block
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

Code Block
widg.raise_()

Scroll down text in

Assuming

Code Block
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:

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

Moving text cursor with repaint() works immidiately:

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

Set optimal table-widget size

Code Block
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:

Code Block

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

Code Block

    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

Code Block

    import tempfile    
    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,'.ppm')) 
            self.setPixmapForImage()

Supported in QImage formats:

Format	Description	Qt's support
BMP	Windows Bitmap	Read/write
GIF	Graphic Interchange Format (optional)	Read
JPG	Joint Photographic Experts Group	Read/write
JPEG	Joint Photographic Experts Group	Read/write
PNG	Portable Network Graphics	Read/write
PBM	Portable Bitmap	Read
PGM	Portable Graymap	Read
PPM	Portable Pixmap	Read/write
TIFF	Tagged Image File Format	Read/write
XBM	X11 Bitmap	Read/write
XPM	X11 Pixmap	Read/write

Grab entire monitor window

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

Load image from file

Code Block
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

Code Block

    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

Code Block
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

Code Block

    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

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

Get window size and position

Global (top-left) point of the window on monitor:

point = self.mapToGlobal(QtCore.QPoint(0,0)) - changing in resizeEvent(...) and moveEvent(...)

x,y,w,h = size.size().x(), size.size().y(), size.size().width(), size.size().height()

where - w and h changing in resizeEvent(...),

x,y changing in moveEvent(...) only.

Window relative dims: rect = self.rect() - changing in resizeEvent(...)

Show image in QtGui.QGraphicsView

QGraphicsView is a class with scrolled graph window...

Repaint widget immediately when its property is changed

When QPushButton is pressed and connected method is called, all button properties stay unchanged until the method. In order to see current changes one has to repaint widget. For example:

Code Block
self.but_elog.setStyleSheet(cp.styleButton) self.but_elog.setEnabled(False) self.repaint()

Dialog boxes

For password

Code Block

    app = QtGui.QApplication(sys.argv)
    w = QtGui.QInputDialog()
    w.show()
    msg = 'To use %s and submitt messages in ELog\nauthentication for user %s is required\nPassword:' % (sys.argv[0], opts.usr)
    text, ok = w.getText(None, 'Authentication', msg, QtGui.QLineEdit.Password)
    w.close()
...

Graphics in PyQt4

Code Block

...
        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

Code Block

    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

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

Tooltips

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

Matplotlib

In examples below we assume

Code Block

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

Code Block
fig.savefig(fname, dpi=240)

Clear figure

Code Block
fig.clear()

Graphic

Code Block
import pyimgalgos.Graphics as gr axes.clear() axes.plot(xarr1, yarr1, '-r', xarr2, yarr2, '-g') gr.show(mode='do_not_hold')

Histogram

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

Image (with colorbar)

Code Block

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

Code Block

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

Code Block
axes = fig.add_subplot(111)

or

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

Make figure with non-equal subplots

Code Block
# 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:

Code Block

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

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

Draw line

Code Block
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

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

Axis without tick-labels

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

Rotate axis tick-labels

Code Block
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

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

Change axis tick-label font size

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

Axes labels and size

Code Block
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:

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

Text in axes

Code Block
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

Code Block
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

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

Log scale methods

Log values:

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

Log scale axes:

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

Log scale image data:

Code Block
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):

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

Plot histogram with log bin size:

Code Block
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

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

Add unicode symbols in string

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

Get canvas and connect it with mouse buttons

Code Block

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:

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

Check and set backend

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

Get the current matplotlib figure window position on monitor

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

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

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

or

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

For our backend starting from python 2.7.2:

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

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

Code Block
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

Code Block
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

Code Block

        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"

Code Block
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

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

Emit your own signal in PyQt4

Code Block

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

Code Block

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

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

Load numpy array from text file

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

Load numpy array from *.npy file

Code Block
nparr = np.load('arr.npy')

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

Save numpy arrays

Code Block
np.savetxt(fname, array) # , fmt='%f') np.save(fname, array) np.savez(fname, [array1, array2,...])

Save image in 8-bit TIFF file

Code Block

bgColor	#DDFFFF

import scipy.misc as scim
    scim.imsave('fname.tiff', arr2d)

Other supported formats: gif, pdf, png, jpeg, eps

Check tiff file

To check tiff file format one may use command:

% identify -verbose <file-name>.tiff

Save image in 16-bit TIFF file

Code Block

bgColor	#DDFFFF

import Image
img = Image.fromarray(arr.astype(np.int16))  # or int32
img.save('fname.tiff')

Read image from TIFF file

Code Block

bgColor	#DDFFFF

import scipy.misc as scim
    arr2d = scim.imread('fname.tiff')

2-d Array rotation by n*90 degree

Code Block

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

a = np.arange(12.).reshape((4, 3))
print 'Input array a=\n',a
print 'rotation for  90 flipud(a.T)=\n',np.flipud(a.T)
print 'rotation for 180 flipud(np.fliplr(a))=\n',np.flipud(np.fliplr(a))
print 'rotation for 270 fliplr(a.T)=\n',np.fliplr(a.T)

Fill histograms using np.bincount

Code Block

binstat = np.bincount(self.rbinind.flatten(), weights=self.mask.flatten(), minlength=self.rrange[2])
bin_integral = np.bincount(self.rbinind.flatten(), weights=image.flatten(), minlength=self.rrange[2])

Use np.select

Code Block
V = np.array(...) Vmin, Vmax, Nbins1 <--- scalar valuer indarr = np.int32( factor * (V-Vmin) ) arr = np.select([V==Vmax, indarr<0, indarr>Nbins1], [Nbins1, 0, 0], default=indarr)

protected division:

Code Block

def divideZeroProteced(nda_num, nda_den, val_subst_zero=0) :
    pro_num = np.select([nda_den==0], [val_subst_zero], default=nda_num)
    pro_den = np.select([nda_den==0], [1],              default=nda_den)
    return pro_num / pro_den

SciPy

Import

Code Block
#!/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:

Code Block

#!/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()

Code Block


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

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Key

Content

Python tricks

Parsing of input parameters

Parsing "on knees"

Use OptionParser

Manipulation with directories and files

Dictionaris, Lists, etc

Make dictionary from two lists

Sorted list

Parsing the pathname

Useful string parsing options

Exceptions

Raise exceprion

Catch exception

Python - useful references

Built-in functions

setattr - gives dynamic variables in python

PyQt4

How to open/close/move other GUI window?

User defined exception

Manipulation with directories and files

Access to files in the derectory

How to close window and delete object?

Matplotlib

How to draw histogram

How to draw graphic

How to define subplot with empty axes

How to make figure with non-equal subplots

How to draw line

How to draw axis without labels

How to rotate axis labels

How to set a number of ticks along the axis

How to change axis label position on the plot

How to draw a color bar as a separate sub-plot

How draw text

At the edge of matplotlib and PyQt4

How to get the current matplotlib figure window position on monitor

How to move the matplotlib figure window in certain (x,y) position

How to move the matplotlib figure window on top (of all pileup windows)

How to add figure as a widget of the QtGui

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

How to receive a signal in program when close window by the click on "X"

How to close figure from program call

Parsing the pathname

Join list of strings

Join path and name

Check if string contains pattern

String alignment

Useful string parsing options

String formatting

Class string properties

Class name

Function name

Function parameters

Converting integer to bin(), oct(), hex() string

Time stamp

Set PYTHONPATH

Replace symbols in string

List of comprehension

map - built-in method

Constructor, destructor etc.

Polymorphism

Derived class initialization

Create/save temporary file

Good example of __main__

Virtualenv

Python - useful references

Built-in functions

setattr, getattr - set/get dynamic variables in python

PyQt4

Know How

PyQt4 class references

Open/close/move other GUI window

Close window and delete object

Good example of main