def process():
if len(sys.argv) <= 1: # default behavior, run general test
print ""
nfail = module_test_lib.num_import_failures(verb=2)
print "\nnumber of python import failures = %d\n" % nfail
return nfail
# create elemnnt and initialize options
MT = ModuleTest()
MT.init_opts()
# read options, return on terminal option or bad usage
rv = MT.read_opts()
if rv != None:
if rv: MT.show_failed_command()
return rv
# apply options
rv = MT.process_opts()
if rv != None:
if rv: MT.show_failed_command()
return rv
# do stuff
rv = MT.execute()
if rv != None:
if rv: MT.show_failed_command()
return rv
def process():
if len(sys.argv) <= 1: # default behavior, run general test
print ""
nfail = module_test_lib.num_import_failures(verb=2)
print "\nnumber of python import failures = %d\n" % nfail
return nfail
# create elemnnt and initialize options
MT = ModuleTest()
MT.init_opts()
# read options, return on terminal option or bad usage
rv = MT.read_opts()
if rv != None:
if rv: MT.show_failed_command()
return rv
# apply options
rv = MT.process_opts()
if rv != None:
if rv: MT.show_failed_command()
return rv
# do stuff
rv = MT.execute()
if rv != None:
if rv: MT.show_failed_command()
return rv
def __init__(self, sport, verb=1):
global g_SER # global reference for serial library
# see if the serial library is available
if module_test_lib.num_import_failures(['serial']): return None
import serial
g_SER = serial
# main variables
self.verb = verb # verbose level
self.port_file = sport # file for serial port
self.data_port = None # serial data port
self.swap = 0 # whether to swap serial bytes
if self.verb > 1: print '++ initializing serial interface %s...' % sport
def __init__(self, sport, verb=1):
global g_SER # global reference for serial library
# see if the serial library is available
if module_test_lib.num_import_failures(['serial']): return None
import serial
g_SER = serial
# main variables
self.verb = verb # verbose level
self.port_file = sport # file for serial port
self.data_port = None # serial data port
self.swap = 0 # whether to swap serial bytes
if self.verb > 1: print('++ initializing serial interface %s...' % sport)
def set_demo_gui(self):
"""create the GUI for display of the demo data"""
testlibs = ['numpy', 'wx']
if module_test_lib.num_import_failures(testlibs): sys.exit(1)
import numpy as N, wx
import lib_RR_plot as LPLOT
self.wx_app = wx.App()
self.demo_frame = LPLOT.CanvasFrame(title='receiver demo')
self.demo_frame.EnableCloseButton(True)
self.demo_frame.Show(True)
self.demo_frame.style = 'bar'
self.demo_frame.xlabel = 'most recent 10 TRs'
self.demo_frame.ylabel = 'scaled diff_ratio'
# for the current demo, set an ranges for 10 numbers in [0,10]
if self.demo_frame.style == 'graph':
self.demo_frame.set_limits(0,9.1,-0.1,10.1)
elif self.demo_frame.style == 'bar':
self.demo_frame.set_limits(0,10.1,-0.1,10.1)
def set_demo_gui(self):
"""create the GUI for display of the demo data"""
testlibs = ['numpy', 'wx']
if module_test_lib.num_import_failures(testlibs): sys.exit(1)
import numpy as N, wx
import lib_RR_plot as LPLOT
self.wx_app = wx.App()
self.demo_frame = LPLOT.CanvasFrame(title='receiver demo')
self.demo_frame.EnableCloseButton(True)
self.demo_frame.Show(True)
self.demo_frame.style = 'bar'
self.demo_frame.xlabel = 'most recent 10 TRs'
self.demo_frame.ylabel = 'scaled diff_ratio'
# for the current demo, set an ranges for 10 numbers in [0,10]
if self.demo_frame.style == 'graph':
self.demo_frame.set_limits(0,9.1,-0.1,10.1)
elif self.demo_frame.style == 'bar':
self.demo_frame.set_limits(0,10.1,-0.1,10.1)
def execute(self):
if self.show_pyver:
if self.verb <= 1:
vlist = sys.version.split()
vstr = vlist[0]
else:
vstr = sys.version
print 'python version: %s' % vstr
if self.show_platform:
try:
import platform
print 'platform: %s' % platform.platform()
except: print 'platform: ** module not found'
if self.show_modtest:
nfail = module_test_lib.num_import_failures(self.modlist,
details=1,verb=self.verb)
print "\nnumber of python import failures = %d\n" % nfail
return None
def set_demo_gui(self):
"""create the GUI for display of the demo data"""
testlibs = ["numpy", "wx"]
if module_test_lib.num_import_failures(testlibs):
return 1
try:
import numpy as N, wx
import lib_RR_plot as LPLOT
except:
return 1
self.wx_app = wx.App()
self.demo_frame = LPLOT.CanvasFrame(title="receiver demo")
self.demo_frame.EnableCloseButton(True)
self.demo_frame.Show(True)
self.demo_frame.style = "bar"
self.demo_frame.xlabel = "most recent 10 TRs"
self.demo_frame.ylabel = "scaled diff_ratio"
# for the current demo, set an ranges for 10 numbers in [0,10]
if self.demo_frame.style == "graph":
self.demo_frame.set_limits(0, 9.1, -0.1, 10.1)
elif self.demo_frame.style == "bar":
self.demo_frame.set_limits(0, 10.1, -0.1, 10.1)
def execute(self):
if self.show_pyver:
if self.verb <= 1:
vlist = sys.version.split()
vstr = vlist[0]
else:
vstr = sys.version
print 'python version: %s' % vstr
if self.show_platform:
try:
import platform
print 'platform: %s' % platform.platform()
except:
print 'platform: ** module not found'
if self.show_modtest:
nfail = module_test_lib.num_import_failures(self.modlist,
details=1,
verb=self.verb)
print "\nnumber of python import failures = %d\n" % nfail
return None
def test_libraries(self,verb=2):
"""test for existence of needed python libraries"""
import module_test_lib as MLT
libs = ['os', 'gc', 'numpy', 'wx', 'matplotlib', 'scipy']
if MLT.num_import_failures(libs,details=1,verb=verb): return 1
else: return 0
#!/usr/bin/env python
# a basic realtime_receiver plotting library
import sys, os
# verify system libraries
import module_test_lib
g_testlibs = ['gc', 'numpy', 'wx', 'matplotlib']
if module_test_lib.num_import_failures(g_testlibs, details=0):
print """
-- for details, consider xmat_tool -test_libs
-- also, many computations do not require the GUI
(e.g. 'xmat_tool -load_xmat X.xmat.1D -show_cormat_warnings')
"""
sys.exit(1)
import numpy as N
import gc
# must use matplotlib with wx, not pylab
import wx
import matplotlib
matplotlib.use('WX')
# set some resource font values
matplotlib.rc('axes', titlesize=11)
matplotlib.rc('axes', labelsize=9)
matplotlib.rc('xtick', labelsize=8)
matplotlib.rc('ytick', labelsize=7)
#!/usr/bin/env python
# python3 status: started
# library for performing various system checks
import os, sys
import module_test_lib as MT
# test dependency libs before proceeding
# note: platform came with python 2.3
testlibs = ['platform', 'afni_base', 'afni_util']
if MT.num_import_failures(testlibs):
sys.exit(1)
import platform, glob
import afni_base as BASE
import afni_util as UTIL
class SysInfo:
"""system info class"""
def __init__(self, data_root='', verb=1):
self.system = platform.system()
self.home_dir = os.environ['HOME']
self.data_root = data_root
self.verb = verb
self.afni_ver = ''
self.afni_label = ''
def set_demo_gui(self):
"""create the GUI for display of the demo data"""
testlibs = ['numpy', 'wx']
if module_test_lib.num_import_failures(testlibs): sys.exit(1)
import numpy as N, wx
#!/usr/bin/env python
import sys
import module_test_lib
g_testlibs = ['sys', 'math', 'numpy']
if module_test_lib.num_import_failures(g_testlibs): sys.exit(1)
# import libraries
import math
import copy
import numpy as N
import afni_util as UTIL
import lib_textdata as TD
class AfniXmat:
def __init__(self, filename="", from_mat=0, matrix=None, verb=1):
"""numpy matrix class
init from filename or matrix,
filename : 1D file to read in as matrix
from_mat : use matrix for initialization (numpy or [])
matrix : Numpy matrix to use if from_mat is set
verb : verbose level of operations
mat : data
fname : filename
rows, cols : dimensions
labels : simple text labels
groups : list: -1 (baseline), 0 (motion), else reg index
#!/usr/bin/env python
# library for performing various system checks
import os, sys
import module_test_lib as MT
# test dependency libs before proceeding
# note: platform came with python 2.3
testlibs = ['platform', 'afni_base', 'afni_util']
if MT.num_import_failures(testlibs):
sys.exit(1)
import platform, glob
import afni_base as BASE
import afni_util as UTIL
class SysInfo:
"""system info class"""
def __init__(self, data_root='', verb=1):
self.system = platform.system()
self.home_dir = os.environ['HOME']
self.data_root = data_root
self.verb = verb
self.afni_ver = ''
self.os_dist = ''
self.comments = [] # comments to print at the end
#!/usr/bin/env python
# basically, a GUI to write an afni_proc.py command
import sys, os, copy, math
# system libraries : test, then import as local symbols
import module_test_lib
testlibs = ['copy', 'signal']
if module_test_lib.num_import_failures(testlibs): sys.exit(1)
import copy
import afni_util as UTIL
import lib_subjects as SUBJ
import lib_vars_object as VO
import lib_uber_skel as USKEL
import option_list as OPT
g_command_help = """
===========================================================================
uber_skel.py - sample uber processing program
(based on uber_align_test.py, version 0.2)
usage: uber_skel.py
---
This help describes only the command line options to this program, which
enables one to:
- initialize user variables (for GUI or command line)
#!/usr/bin/env python
# basically, a GUI to write an afni_proc.py command
import sys, os, copy, math
# system libraries : test, then import as local symbols
import module_test_lib
testlibs = ["copy", "signal"]
if module_test_lib.num_import_failures(testlibs):
sys.exit(1)
import copy
import afni_util as UTIL
import lib_subjects as SUBJ
import lib_uber_align as UALIGN
import option_list as OPT
g_command_help = """
===========================================================================
uber_align_test.py - generate script to test anat/EPI alignment
usage: uber_align_test.py
---
This help describes only the command line options to this program, which
enables one to:
- initialize user variables (for GUI or command line)
#!/usr/bin/env python
# a basic realtime_receiver plotting library
import sys, os
# verify system libraries
import module_test_lib
g_testlibs = ['gc', 'numpy', 'wx', 'matplotlib']
if module_test_lib.num_import_failures(g_testlibs,details=0):
print """
-- for details, consider xmat_tool -test_libs
-- also, many computations do not require the GUI
(e.g. 'xmat_tool -load_xmat X.xmat.1D -show_cormat_warnings')
"""
sys.exit(1)
import numpy as N
import gc
# must use matplotlib with wx, not pylab
import wx
import matplotlib
matplotlib.use('WX')
# set some resource font values
matplotlib.rc('axes',titlesize=11)
matplotlib.rc('axes',labelsize=9)
matplotlib.rc('xtick',labelsize=8)
matplotlib.rc('ytick',labelsize=7)
def test_libraries(self, verb=2):
"""test for existence of needed python libraries"""
import module_test_lib as MLT
libs = ['os', 'gc', 'numpy', 'wx', 'matplotlib', 'scipy']
if MLT.num_import_failures(libs, details=1, verb=verb): return 1
else: return 0
