On 30 April 2010 21:21, Pavel Kaderavek <pavel.kaderavek@xxxxxxxxx>
wrote:
Hi,
I tried to do the changes in the __init__ function of Mf class in the
file
maths_fns/mf.py.
I am not sure about the way of initialization you described in the
previous
mail. I understand that it is necessary to initialize the lists between
the
loops, but I would do it in this way:
self.data[i].interactions = zeros(self.num_interactions[i], float64)
Hi,
It would be best to do this differently. The interactions will be
part of self.data. This structure can be turned into a 2D list of
lists - i.e. like a matrix where each row corresponds to one
interaction and each column corresponds to an isolated spin system.
You do this by replacing:
# Create the data array used to store data.
self.data = []
for i in xrange(self.num_spins):
# Total number of ri.
self.total_num_ri = self.total_num_ri + num_ri[i]
# The ratio of gyromagnetic ratios.
g_ratio = gh[i] / gx[i]
# Append the class instance Data to the data array.
self.data.append(Data())
...
with:
# Create the data list of lists used to store the interaction
and spin specific data.
self.data = []
for int_index in xrange(self.num_interactions):
# Add an empty list for the interaction.
self.data.append([])
# Loop over the spins.
for spin_index in xrange(self.num_spins):
# Total number of ri (only sum for the first interaction).
if int_index == 0:
self.total_num_ri = self.total_num_ri +
num_ri[spin_index]
# The ratio of gyromagnetic ratios.
g_ratio = gh[int_index][spin_index] /
gx[int_index][spin_index]
# Append the class instance Data to the interaction
list for this spin.
self.data[int_index].append(Data())
This will set up the correct data structure.
I think I can avoid procedure inside the second loop where you suggest
to a
new data
container initialise and append to the list. Now I can just fill the
list:
for j in xrange(self.num_interactions[i]):
self.data[i].interactions[j]=interactions[i][j]
Am I wrong? Did I misunderstand something?
This would work, but the interactions structure is not necessary - it
can be directly part of self.data. The interaction can be considered
higher level than the spin, so you can collapse this to:
self.data[interaction_index][spin_index]
This list of lists is much simpler and easier to maintain in the future.
Moreover, I found that in the __init__ function is necessary to extend
the
dimension of frequencies per field strength. They will be different
between
(for example) CC and CH interactions. So, what do you think about this:
self.data[i].frq_list = zeros((self.num_interactions[i], num_frq[i],
5),
float64)
for j in xrange(num_frq[i]):
frqH = 2.0 * pi * frq[i][j]
frqX = frqH / g_ratio
for k in xrange(self.num_interactions[i]):
frqY = frqH * self.data[i].gratio_ext[k] / gh[i]
self.data[i].frq_list[k, j, 1] = frqX
self.data[i].frq_list[k, j, 2] = frqY - frqX
The CC and CH interaction would be in different Data containers, so
this is not necessary. They would be in:
self.data[CC_index][spin_index]
self.data[CH_index][spin_index]
Each interaction and each spin has it's own data container in
self.data[x][y], therefore almost all the rest of the code in math_fns
remains identical and untouched.
Small question at the end:
Can it be included in the same patch - both changes belongs to changes
in
one function or is it too large step?
It would be best to have separate patches. That way they can be
individually checked and optimised. In programing in a group
environment, it is recommended that each patch/commit should contain
only one concept. If there are two unrelated changes in a patch, it
is standard practice that the patch creator is asked to split it up
and resend it. If it was directly committed, that commit will be
reverted. And small patches are much easier to have accepted.
One thing I would highly recommend for the start is to have a test RNA
data set. This should be of 2 or 3 spins, and where you know what the
result is. Normally synthetic data is best, but otherwise results
published from a reliable source can be used. A script performing
model-free analysis is then written. The aim is to have a data set
and script that will be used to check if the code is working. We then
add it to the test suite as a system test. This should be done before
anything else. This test will then, from now until the death of
relax, enforce that this analysis always works for all users. In the
test suite system we can exactly and easily check the optimisation
results. This is a very useful way of coding because once the test
passes - then you know that the code is complete!
Cheers,
Edward
Re: CST branch