Windows: Upgrade shipped numpy version

[Martyn Gigg]

Make sure we don't lag too far behind the current version.

[Martyn Gigg]

And ship a compatible version of scipy at the same time.

[Martyn Gigg]

Remove numpy 1.5.1. Refs #5760

Ensure all old files have been removed before updating.

Changeset: ce754ad12abfa5a3baef3abe718f762d88d596c5

[Martyn Gigg]

Upgrade numpy to 1.6.2 Refs #5760

Built with Visual Studio 10 and includes debug libraries.

Changeset: 74f570c4b9336fc183585d3683932b6f95a71e59

[Martyn Gigg]

Add numpy f2py scripts. Refs #5760

Changeset: 2aed79497d406e80bca283fbe56199fe451a0f78

[Martyn Gigg]

Add patched msvccompiler (+patch) to build with MSVC 2010. Refs #5760

Changeset: 7e3f3ef142e23545f259b9134508c45ca532843d

[Martyn Gigg]

Add batch file to build numpy with MSVC. Refs #5760

Changeset: 083ae98b325325cd7edb9bf0fd1a78c8c2fc3d46

[Martyn Gigg]

Remove numpy 1.5.1 Refs #5760

Changeset: 69e5b5d2d380fdee8cb317087205d4ea7b464510

[Martyn Gigg]

Add ctypes debug module for Python. Refs #5760

It can be useful to have it in debug.

Changeset: 6a4f96cd83edbb54ef84de8c84ebf51374f3725e

[Martyn Gigg]

Add f2py scripts. Refs #5760

Changeset: 01cc66c1a74157e6406baedef62e6fc79caf5149

[Martyn Gigg]

Update precompiled Inelastic fortran to use numpy 1.6.2. Refs #5760

Changeset: 94db7996dd6f1d6b09b2f9484f69995bc55347cf

[Martyn Gigg]

Force recompile of numpy pyc modules. Refs #5760

First import of old ones seem to mark them as changed.

Changeset: 6e87605f4e98686ee64f420e8c420dca287bc404

[Martyn Gigg]

Add scipy-0.11. Refs #5760

Changeset: 99d23ee44553565a16f5220f912eb3e5294d06db

[Nick Draper]

NumPy Tests

NumPy Version - Passed

import numpy as nm
print nm.version.version

1.6.2

NumPy array - Passed

from numpy import *
a= arange(12)
a=a.reshape(3,2,2)
print a

[[[ 0  1]
  [ 2  3]]

 [[ 4  5]
  [ 6  7]]

 [[ 8  9]
  [10 11]]]

Transpose - Passed

a=array([[1,2,3],[4,5,6]])
print a.shape
b=a.transpose()
print b.shape
(2L, 3L)
(3L, 2L)

[Nick Draper]

NumPy with workspace data - Passed

ws=Load("GEM38370")
a=ws.readY(0)
print a.shape
b= a.reshape(505,10)
print b.shape
(5050L,)
(505L, 10L)

[Nick Draper]

SciPy

Version - passed

import scipy
print scipy.version.version
0.11.0

convolve - Passed

from scipy import *
x=r_[1:4]
h1=zeros(15)
h1[0] =1
h2=zeros(15)
h2[6] =1
h3=zeros(15)
h3[12] =1
print convolve(h1+h2+h3,x)
[ 1.  2.  3.  0.  0.  0.  1.  2.  3.  0.  0.  0.  1.  2.  3.  0.  0.]

Optimize - Failed

from pylab import *
from numpy import *
from scipy.optimize import leastsq

## Parametric function: 'v' is the parameter vector, 'x' the independent varible
fp = lambda v, x: v[0]/(x**v[1])*sin(v[2]*x)

## Noisy function (used to generate data to fit)
v_real = [1.5, 0.1, 2.]
fn = lambda x: fp(v_real, x)

## Error function
e = lambda v, x, y: (fp(v,x)-y)

## Generating noisy data to fit
n = 30
xmin = 0.1
xmax = 5
x = linspace(xmin,xmax,n)
y = fn(x) + rand(len(x))*0.2*(fn(x).max()-fn(x).min())

## Initial parameter value
v0 = [3., 1, 4.]

## Fitting
v, success = leastsq(e, v0, args=(x,y), maxfev=10000)

## Plot
def plot_fit():
    print 'Estimater parameters: ', v
    print 'Real parameters: ', v_real
    X = linspace(xmin,xmax,n*5)
    plot(x,y,'ro', X, fp(v,X))

plot_fit()
show()

Error on line 3:
ImportError: DLL load failed: The specified module could not be found.
  at line 3 in ''
  caused by line 144 in 'C:\MantidInstall\bin\lib\site-packages\scipy\optimize\__init__.py'
  caused by line 30 in 'C:\MantidInstall\bin\lib\site-packages\scipy\optimize\optimize.py'
  caused by line 14 in 'C:\MantidInstall\bin\lib\site-packages\scipy\optimize\linesearch.py'

[Martyn Gigg]

Rebuilt scipy .pyd to link with gfortran statically. Refs #5760

Changeset: e9804d3749bb49b17c8de69ae4f69be5832dae43

[Martyn Gigg]

Only keep numpy .pyc files in repo Refs #5760

If the py files are present then they pyc files keep getting recompiled when numpy is imported and look modified to git. The correct procedure would be to include only py files & compile on packaging. Left for future work.

Changeset: 18bcdf9c605bccfe58dc76790a8e18c56c88f8c0

[Martyn Gigg]

Only keep numpy .pyc files in repo Refs #5760

If the py files are present then they pyc files keep getting recompiled when numpy is imported and look modified to git. The correct procedure would be to include only py files & compile on packaging. Left for future work.

Changeset: 2880d4ea887ff9ff308123ac9a4581c5997554b5

[Martyn Gigg]

Replace numpy & scipy with MKL variants. Refs #5760

It turns out we can redistribute as we have an appropriate license.

Changeset: 44a98a192e249ccf95ae790413c04b71112e6393

[Martyn Gigg]

Replace numpy & scipy with MKL variants. Refs #5760

Consistent with 64-bit platform then.

Changeset: ce44725367e30ffdd50fd0ab7f04c1384113c1be

[Martyn Gigg]

Add gfortran libraries for mingw for Inelastic pyd files. Refs #5760

Changeset: 8228335ca81316daad927bbf10071f2ae895fdc2

[Martyn Gigg]

Install fortran libraries for inelastic modules... Refs #5760

on win32. Not quite sure how these have worked in the past without them, they must have been statically linked but the latest f2py seems to dynamically link them.

Changeset: b532aa2ddadbea990e2bb42be475f5e73b6803fa

[Martyn Gigg]

Tester: I've had to slightly modifiy the test script to do the plotting. Anything that will perform a GUI command needs to be wrapped with our function that ensures it happens on the correct thread.

There is also a mode under the execute menu for serialised running that will work but that's less ideal I think.

Should I think about having an alias for the threadsafe_call function with a more understandable name: gui_call or something?

from pylab import *
from numpy import *
from scipy.optimize import leastsq

## Parametric function: 'v' is the parameter vector, 'x' the independent varible
fp = lambda v, x: v[0]/(x**v[1])*sin(v[2]*x)

## Noisy function (used to generate data to fit)
v_real = [1.5, 0.1, 2.]
fn = lambda x: fp(v_real, x)

## Error function
e = lambda v, x, y: (fp(v,x)-y)

## Generating noisy data to fit
n = 30
xmin = 0.1
xmax = 5
x = linspace(xmin,xmax,n)
y = fn(x) + rand(len(x))*0.2*(fn(x).max()-fn(x).min())

## Initial parameter value
v0 = [3., 1, 4.]

## Fitting
v, success = leastsq(e, v0, args=(x,y), maxfev=10000)

## Plot
def plot_fit():
    print 'Estimater parameters: ', v
    print 'Real parameters: ', v_real
    X = linspace(xmin,xmax,n*5)
    plot(x,y,'ro', X, fp(v,X))

threadsafe_call(plot_fit)
threadsafe_call(show)

[Nick Draper]

Still fails with same error on version 2.2.1133

[Martyn Gigg]

Put numpy & scipy dependencies in bin on packaging. Refs #5760

That way they both can find them.

Changeset: 65e0e07cf6f2aea9a4e722653bc0fe5a25b41e5a

[Martyn Gigg]

Update precompiled Inelastic fortran to use numpy 1.6.2. Refs #5760

Changeset: 94db7996dd6f1d6b09b2f9484f69995bc55347cf

[Martyn Gigg]

Install fortran libraries for inelastic modules... Refs #5760

on win32. Not quite sure how these have worked in the past without them, they must have been statically linked but the latest f2py seems to dynamically link them.

Changeset: b532aa2ddadbea990e2bb42be475f5e73b6803fa

[Martyn Gigg]

Put numpy & scipy dependencies in bin on packaging. Refs #5760

That way they both can find them.

Changeset: 65e0e07cf6f2aea9a4e722653bc0fe5a25b41e5a

[Martyn Gigg]

Install fortran libraries for inelastic modules... Refs #5760

on win32. Not quite sure how these have worked in the past without them, they must have been statically linked but the latest f2py seems to dynamically link them.

Changeset: b532aa2ddadbea990e2bb42be475f5e73b6803fa

[Martyn Gigg]

Put numpy & scipy dependencies in bin on packaging. Refs #5760

That way they both can find them.

Changeset: 65e0e07cf6f2aea9a4e722653bc0fe5a25b41e5a

[Stuart Campbell]

This ticket has been transferred to github issue ​6606