From fbbbf8d630e44978c94b03b63f665648ba71fd4f Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Wed, 29 Oct 2014 23:41:46 +0100
Subject: [PATCH] Fixed m and n controversy: m: i'm'age n:
i'n'put
---
pyramid/costfunction.py | 10 ++++++---
pyramid/dataset.py | 13 ++++++-----
pyramid/forwardmodel.py | 10 ++++-----
pyramid/magdata.py | 8 +++----
pyramid/phasemapper.py | 50 ++++++++++++++++++++---------------------
pyramid/projector.py | 8 +++----
6 files changed, 52 insertions(+), 47 deletions(-)
diff --git a/pyramid/costfunction.py b/pyramid/costfunction.py
index ad7c226..ce113f9 100644
--- a/pyramid/costfunction.py
+++ b/pyramid/costfunction.py
@@ -40,6 +40,10 @@ class Costfunction(object):
Se_inv : :class:`~numpy.ndarray` (N=2), optional
Inverted covariance matrix of the measurement errors. The matrix has size `NxN` with N
being the length of the targetvector y (vectorized phase map information).
+ m: int
+ Size of the image space.
+ n: int
+ Size of the input space.
'''
@@ -53,8 +57,8 @@ class Costfunction(object):
# Extract important information:
self.y = data_set.phase_vec
self.Se_inv = data_set.Se_inv
- self.n = data_set.n * 3
- self.m = len(self.y)
+ self.n = data_set.n
+ self.m = data_set.m
self.LOG.debug('Created '+str(self))
def __repr__(self):
@@ -161,7 +165,7 @@ class CFAdapterScipyCG(LinearOperator):
@property
def shape(self):
- return (self.cost.data_set.m, self.cost.data_set.m)
+ return (self.cost.data_set.n, self.cost.data_set.n)
@property
def dtype(self):
diff --git a/pyramid/dataset.py b/pyramid/dataset.py
index fd5fb49..39d528c 100644
--- a/pyramid/dataset.py
+++ b/pyramid/dataset.py
@@ -46,22 +46,23 @@ class DataSet(object):
A list of all stored :class:`~.PhaseMap` objects.
phase_vec: :class:`~numpy.ndarray` (N=1)
The concatenaded, vectorized phase of all ;class:`~.PhaseMap` objects.
- n: int
- Size of the image space.
m: int
+ Size of the image space.
+ n: int
Size of the input space.
+
'''
LOG = logging.getLogger(__name__+'.DataSet')
@property
- def n(self):
+ def m(self):
return np.sum([len(p.phase_vec) for p in self.phase_maps])
@property
def Se_inv(self):
# TODO: better implementation, maybe get-method? more flexible? input in append?
- return sp.eye(self.n)
+ return sp.eye(self.m)
@property
def phase_vec(self):
@@ -88,9 +89,9 @@ class DataSet(object):
'Dimension has to be a tuple of length 3!'
if mask is not None:
assert mask.shape == dim, 'Mask dimensions must match!'
- self.m = 3 * np.sum(self.mask)
+ self.n = 3 * np.sum(self.mask)
else:
- self.m = 3 * np.prod(dim)
+ self.n = 3 * np.prod(dim)
self.a = a
self.dim = dim
self.b_0 = b_0
diff --git a/pyramid/forwardmodel.py b/pyramid/forwardmodel.py
index c48a7f7..8d7d1d5 100644
--- a/pyramid/forwardmodel.py
+++ b/pyramid/forwardmodel.py
@@ -30,9 +30,9 @@ class ForwardModel(object):
The grid spacing in nm.
dim : tuple (N=3)
Dimensions of the 3D magnetic distribution.
- n: int
- Size of the image space. Number of pixels of the 2-dimensional projected grid.
m: int
+ Size of the image space. Number of pixels of the 2-dimensional projected grid.
+ n: int
Size of the input space. Number of voxels of the 3-dimensional grid.
'''
@@ -61,7 +61,7 @@ class ForwardModel(object):
self.LOG.debug('Calling __call__')
self.mag_data.set_vector(x, self.data_set.mask)
# TODO: Multiprocessing
- result = np.zeros(self.n)
+ result = np.zeros(self.m)
hp = self.hook_points
for i, projector in enumerate(self.data_set.projectors):
phase_map = self.phase_mappers[projector.dim_uv](projector(self.mag_data))
@@ -90,7 +90,7 @@ class ForwardModel(object):
'''
self.LOG.debug('Calling jac_dot')
self.mag_data.set_vector(vector, self.data_set.mask)
- result = np.zeros(self.n)
+ result = np.zeros(self.m)
hp = self.hook_points
for i, projector in enumerate(self.data_set.projectors):
mag_vec = self.mag_data.mag_vec
@@ -119,7 +119,7 @@ class ForwardModel(object):
'''
self.LOG.debug('Calling jac_T_dot')
- result = np.zeros(self.m)
+ result = np.zeros(self.n)
hp = self.hook_points
for i, projector in enumerate(self.data_set.projectors):
vec = vector[hp[i]:hp[i+1]]
diff --git a/pyramid/magdata.py b/pyramid/magdata.py
index 5989153..cfb0ddf 100644
--- a/pyramid/magdata.py
+++ b/pyramid/magdata.py
@@ -281,9 +281,9 @@ class MagData(object):
Order is: first all `x`-, then all `y`-, then all `z`-components.
'''
- return np.reshape([self.magnitude[2][mask],
+ return np.reshape([self.magnitude[0][mask],
self.magnitude[1][mask],
- self.magnitude[0][mask]], -1)
+ self.magnitude[2][mask]], -1)
def set_vector(self, vector, mask=None):
'''Set the magnetic components of the masked pixels to the values specified by `vector`.
@@ -304,9 +304,9 @@ class MagData(object):
assert np.size(vector) % 3 == 0, 'Vector has to contain all 3 components for every pixel!'
count = np.size(vector)/3
if mask is not None:
- self.magnitude[2][mask] = vector[:count] # x-component
+ self.magnitude[0][mask] = vector[:count] # x-component
self.magnitude[1][mask] = vector[count:2*count] # y-component
- self.magnitude[0][mask] = vector[2*count:] # z-component
+ self.magnitude[2][mask] = vector[2*count:] # z-component
else:
self.mag_vec = vector
diff --git a/pyramid/phasemapper.py b/pyramid/phasemapper.py
index 1d4205a..f121e3b 100644
--- a/pyramid/phasemapper.py
+++ b/pyramid/phasemapper.py
@@ -75,9 +75,9 @@ class PhaseMapperRDFC(PhaseMapper):
geometry : {'disc', 'slab'}, optional
Elementary geometry which is used for the phase contribution of one pixel.
Default is 'disc'.
- n: int
- Size of the image space.
m: int
+ Size of the image space.
+ n: int
Size of the input space.
'''
@@ -87,8 +87,8 @@ class PhaseMapperRDFC(PhaseMapper):
def __init__(self, kernel):
self.LOG.debug('Calling __init__')
self.kernel = kernel
- self.n = np.prod(kernel.dim_uv)
- self.m = 2 * self.n
+ self.m = np.prod(kernel.dim_uv)
+ self.n = 2 * self.m
self.LOG.debug('Created '+str(self))
def __repr__(self):
@@ -135,8 +135,8 @@ class PhaseMapperRDFC(PhaseMapper):
'''
self.LOG.debug('Calling jac_dot')
- assert len(vector) == self.m, \
- 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.m)
+ assert len(vector) == self.n, \
+ 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.n)
u_mag, v_mag = np.reshape(vector, (2,)+self.kernel.dim_uv)
return self._convolve(u_mag, v_mag)
@@ -157,10 +157,10 @@ class PhaseMapperRDFC(PhaseMapper):
'''
self.LOG.debug('Calling jac_T_dot')
- assert len(vector) == self.n, \
- 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.n)
+ assert len(vector) == self.m, \
+ 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.m)
# TODO: directly? ask Jörn again!
- result = np.zeros(self.m)
+ result = np.zeros(self.n)
nc.jac_T_dot_real_convolve(self.kernel.dim_uv[0], self.kernel.dim_uv[1],
self.kernel.u, self.kernel.v, vector, result)
return result
@@ -204,8 +204,8 @@ class PhaseMapperRDRC(PhaseMapper):
self.kernel = kernel
self.threshold = threshold
self.numcore = numcore
- self.n = np.prod(kernel.dim_uv)
- self.m = 2 * self.n
+ self.m = np.prod(kernel.dim_uv)
+ self.n = 2 * self.m
self.LOG.debug('Created '+str(self))
def __repr__(self):
@@ -266,15 +266,15 @@ class PhaseMapperRDRC(PhaseMapper):
'''
self.LOG.debug('Calling jac_dot')
- assert len(vector) == self.m, \
- 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.m)
+ assert len(vector) == self.n, \
+ 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.n)
v_dim, u_dim = self.kernel.dim_uv
- result = np.zeros(self.n)
+ result = np.zeros(self.m)
if self.numcore:
nc.jac_dot_real_convolve(v_dim, u_dim, self.kernel.u, self.kernel.v, vector, result)
else:
# Iterate over all contributing pixels (numbered consecutively)
- for s in range(self.n): # column-wise (two columns at a time, u- and v-component)
+ for s in range(self.m): # column-wise (two columns at a time, u- and v-component)
i = s % u_dim # u-coordinate of current contributing pixel
j = int(s/u_dim) # v-coordinate of current ccontributing pixel
u_min = (u_dim-1) - i # u_dim-1: center of the kernel
@@ -282,7 +282,7 @@ class PhaseMapperRDRC(PhaseMapper):
v_min = (v_dim-1) - j # v_dim-1: center of the kernel
v_max = (2*v_dim-1) - j # = v_min + v_dim
result += vector[s] * self.kernel.u[v_min:v_max, u_min:u_max].reshape(-1)
- result -= vector[s+self.n] * self.kernel.v[v_min:v_max, u_min:u_max].reshape(-1)
+ result -= vector[s+self.m] * self.kernel.v[v_min:v_max, u_min:u_max].reshape(-1)
return result
def jac_T_dot(self, vector):
@@ -302,15 +302,15 @@ class PhaseMapperRDRC(PhaseMapper):
'''
self.LOG.debug('Calling jac_T_dot')
- assert len(vector) == self.n, \
- 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.n)
+ assert len(vector) == self.m, \
+ 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.m)
v_dim, u_dim = self.dim_uv
- result = np.zeros(self.m)
+ result = np.zeros(self.n)
if self.numcore:
nc.jac_T_dot_real_convolve(v_dim, u_dim, self.kernel.u, self.kernel.v, vector, result)
else:
# Iterate over all contributing pixels (numbered consecutively):
- for s in range(self.n): # row-wise (two rows at a time, u- and v-component)
+ for s in range(self.m): # row-wise (two rows at a time, u- and v-component)
i = s % u_dim # u-coordinate of current contributing pixel
j = int(s/u_dim) # v-coordinate of current contributing pixel
u_min = (u_dim-1) - i # u_dim-1: center of the kernel
@@ -318,7 +318,7 @@ class PhaseMapperRDRC(PhaseMapper):
v_min = (v_dim-1) - j # v_dim-1: center of the kernel
v_max = (2*v_dim-1) - j # = v_min + v_dim
result[s] = np.sum(vector*self.u[v_min:v_max, u_min:u_max].reshape(-1))
- result[s+self.n] = np.sum(vector*-self.v[v_min:v_max, u_min:u_max].reshape(-1))
+ result[s+self.m] = np.sum(vector*-self.v[v_min:v_max, u_min:u_max].reshape(-1))
return result
@@ -356,8 +356,8 @@ class PhaseMapperFDFC(PhaseMapper):
self.dim_uv = dim_uv
self.b_0 = b_0
self.padding = padding
- self.n = np.prod(dim_uv)
- self.m = 2 * self.n
+ self.m = np.prod(dim_uv)
+ self.n = 2 * self.m
self.LOG.debug('Created '+str(self))
def __repr__(self):
@@ -416,8 +416,8 @@ class PhaseMapperFDFC(PhaseMapper):
'''
self.LOG.debug('Calling jac_dot')
- assert len(vector) == self.m, \
- 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.m)
+ assert len(vector) == self.n, \
+ 'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.n)
mag_proj = MagData(self.a, np.zeros((3, 1)+self.dim_uv))
magnitude_proj = self.jac_dot(vector).reshape((2, )+self.dim_uv)
mag_proj.magnitude[1:3, 0, ...] = magnitude_proj
diff --git a/pyramid/projector.py b/pyramid/projector.py
index 09e5260..f40e996 100644
--- a/pyramid/projector.py
+++ b/pyramid/projector.py
@@ -45,9 +45,9 @@ class Projector(object):
coeff : list (N=2)
List containing the six weighting coefficients describing the influence of the 3 components
of a 3-dimensional vector field on the 2 projected components.
- n: int
- Size of the image space.
m: int
+ Size of the image space.
+ n: int
Size of the input space.
'''
@@ -63,8 +63,8 @@ class Projector(object):
self.weight = weight
self.coeff = coeff
self.size_2d, self.size_3d = weight.shape
- self.m = 3 * np.prod(dim)
- self.n = 2 * np.prod(dim_uv)
+ self.n = 3 * np.prod(dim)
+ self.m = 2 * np.prod(dim_uv)
self.LOG.debug('Created '+str(self))
def __repr__(self):
--
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