NIFTy merge requestshttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests2023-09-08T15:17:07Zhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/866Implement likelihood residuals and embrace pytrees in all likelihoods2023-09-08T15:17:07ZGordian EdenhoferImplement likelihood residuals and embrace pytrees in all likelihoodsGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/863demos/getting_started_4: Remove deprecated seaborn plotting2023-09-16T07:45:21ZGordian Edenhoferdemos/getting_started_4: Remove deprecated seaborn plottingGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/860Tweak msc2023-08-14T10:54:25ZPhilipp FrankTweak mscUse batches for convolution and interpolation for speedup.
Change the interface of kernel interpolation: (bool) is_linear -> (str) interpolation_method_in
Provide user specified interpolation method also for the output: interpolation_met...Use batches for convolution and interpolation for speedup.
Change the interface of kernel interpolation: (bool) is_linear -> (str) interpolation_method_in
Provide user specified interpolation method also for the output: interpolation_method_out
Both interpolation methods currently implement nearest neighbor ('nearest') and (multi-)linear interpolation ('linear')Philipp FrankPhilipp Frankhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/859Update gitlab-ci to un-deprecated global variables2023-08-07T09:30:56ZGordian EdenhoferUpdate gitlab-ci to un-deprecated global variablesGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/857Rethink Fields and Sampling2023-08-30T04:40:07ZGordian EdenhoferRethink Fields and SamplingChange two core principles: Transform the NIFTy.re's `Field` class into a simpler `Vector` class and harmonize the sampling to always work with stacked samples instead of list of samples.Change two core principles: Transform the NIFTy.re's `Field` class into a simpler `Vector` class and harmonize the sampling to always work with stacked samples instead of list of samples.Gordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/856Switch to debain:bullseye-slim for CI2023-06-16T10:13:05ZPhilipp FrankSwitch to debain:bullseye-slim for CIPhilipp FrankPhilipp Frankhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/855add hashing for MPI equality check for fields in optimize_kl2023-06-16T09:36:03ZJakob Knollmuelleradd hashing for MPI equality check for fields in optimize_klchecking MPI equality of large fields explicitly can crash and lead to segmentation faults, that's why we introduced the possibility to just compare hashes. We didn't add it to the check in the `_single_value_sample_list` in optimize_kl....checking MPI equality of large fields explicitly can crash and lead to segmentation faults, that's why we introduced the possibility to just compare hashes. We didn't add it to the check in the `_single_value_sample_list` in optimize_kl.py and I run into an issue there.https://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/852Extract values form field at given indices2023-06-12T08:13:19ZJakob RothExtract values form field at given indicesExtracts values from a field at given indices and puts them into an unstructured field. Useful when some indices appear twice (e.g. several measurements at the same location).Extracts values from a field at given indices and puts them into an unstructured field. Useful when some indices appear twice (e.g. several measurements at the same location).Philipp FrankPhilipp Frankhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/851Rethink NIFTy.re.Field (Field -> Vector)2023-07-04T16:36:39ZGordian EdenhoferRethink NIFTy.re.Field (Field -> Vector)Gordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/849OperatorAdapter.jax_expr: Fix casting in recent JAX2023-05-02T14:31:08ZGordian EdenhoferOperatorAdapter.jax_expr: Fix casting in recent JAXGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/848Fix potential color rendering error in multifrequency plotting2023-05-09T16:38:01ZLukas PlatzFix potential color rendering error in multifrequency plottingWhile refactoring the multifrequency plotting, I think I discoverd an error in the wavelength-color mapping.
To test the routine, I created an mf image in which each column contains contribution from only one wavelength. Below are imag...While refactoring the multifrequency plotting, I think I discoverd an error in the wavelength-color mapping.
To test the routine, I created an mf image in which each column contains contribution from only one wavelength. Below are images how the nifty plotting routine in the current `NIFTy_8` branch renders this image ("original") and how my (supposedly) fixed routine does ("new_fixed").
![original](/uploads/91f9a2b3ac0d3fbe3d17c69d9a0a8db8/original.png)
![new_fixed](/uploads/e5dbe3706f7e6b12734eebacb9f6bec5/new_fixed.png)
I expect a test image like described to be rendered into the familiar rainbow colors known of visualizations of the visibible light spectrum, but the original RGB mapping instead produces some red, lots of yellow, some turquise, and lots of violet.
The problem seems to be that the original routine first applies the rgb mapping and *then* the logarithmic "sensitivity" correction, while it should be the other way around. The source branch of this MR contains the code producing the "new_fixed" output.
@mtr @pfrank What do you think? Was the original behavior desireable, or is the new behavior better? I lean towards the latter, if our goal is to map spectral data to the visible spectrum without color distortion.https://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/846Import `TransposeOperator` into NIFTy namespace2023-04-17T07:33:09ZLukas PlatzImport `TransposeOperator` into NIFTy namespaceFor some reason the openly documented `TransposeOperator` is not imported into the NIFTy namespace.
I suspect this is an oversight, therefore this merge request.For some reason the openly documented `TransposeOperator` is not imported into the NIFTy namespace.
I suspect this is an oversight, therefore this merge request.https://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/845Fix pipeline2023-03-17T17:58:30ZGordian EdenhoferFix pipelineGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/843Various small tweaks2023-05-01T18:56:19ZGordian EdenhoferVarious small tweaksGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/842Introduce a more flexible sequential map2023-05-02T13:50:13ZGordian EdenhoferIntroduce a more flexible sequential mapGordian EdenhoferGordian Edenhoferhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/840Reintroduce `plt.figure()` to protect user figures from closing2023-02-22T14:11:28ZLukas PlatzReintroduce `plt.figure()` to protect user figures from closingPhilipp FrankPhilipp Frankhttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/839change from last to latest2023-02-02T16:41:18ZVincent Eberlechange from last to latest#359#359Martin ReineckeMartin Reineckehttps://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/838don't open new fig in every iteration2023-02-13T09:36:48ZJakob Rothdon't open new fig in every iterationCurrently, opimize_kl opens a new figure, when plotting the minisanity history, in every iteration of the optimisation (See this line in the code: https://gitlab.mpcdf.mpg.de/ift/nifty/-/blob/NIFTy_8/src/minimization/optimize_kl.py#L613)...Currently, opimize_kl opens a new figure, when plotting the minisanity history, in every iteration of the optimisation (See this line in the code: https://gitlab.mpcdf.mpg.de/ift/nifty/-/blob/NIFTy_8/src/minimization/optimize_kl.py#L613). After the minisanity plot the figure is cleared but not closed. Thus after an `optimize_kl` run with n iterations, there are n open matplotlib figures. If one calls `plt.show()` after `optimize_kl` n empty figures will open. Here is a small demo:
```
import nifty8 as ift
import matplotlib.pyplot as plt
import numpy as np
from mpi4py import MPI
comm = MPI.COMM_WORLD
master = comm.Get_rank() == 0
############ some nifty with optimize_kl ##############
sp = ift.RGSpace(1)
op = ift.makeOp(ift.full(sp, 1)).ducktape('blub')
d = ift.full(sp, 1.)
n = ift.ScalingOperator(sp, 0.1, np.float64)
lh = ift.GaussianEnergy(d, inverse_covariance=n.inverse) @ op
n_iterations = 3
n_samples = 2
ic_sampling = ift.AbsDeltaEnergyController(name="Sampling (linear)",
deltaE=0.05, iteration_limit=100)
ic_newton = ift.AbsDeltaEnergyController(name='Newton', deltaE=0.5,
convergence_level=2, iteration_limit=35)
ic_sampling_nl = ift.AbsDeltaEnergyController(name='Sampling (nonlin)',
deltaE=0.5, iteration_limit=15,
convergence_level=2)
minimizer = ift.NewtonCG(ic_newton)
minimizer_sampling = ift.NewtonCG(ic_sampling_nl)
samples = ift.optimize_kl(lh, n_iterations, 2,
minimizer, ic_sampling, minimizer_sampling,
output_directory="folder",
comm=comm, plot_energy_history=True,
plot_minisanity_history=True)
#######################################################
x = np.linspace(1,10,100)
plt.plot(x,x**2)
if master:
plt.show()
```
Is there a reason to create a new figure every time? I guess this is a bug. I have removed the `plt.figure()`. Note: also in the energy history we don't have a `plt.figure()`.https://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/836remove note mpi tasks in sample_list2023-01-25T12:09:28ZJakob Rothremove note mpi tasks in sample_listIn the Sample List documentation, we have a note that a sample list has to be loaded with the sample number of MPI tasks with which the Sample List was saved. Actually, this condition is not necessary. The number of MPI tasks does neithe...In the Sample List documentation, we have a note that a sample list has to be loaded with the sample number of MPI tasks with which the Sample List was saved. Actually, this condition is not necessary. The number of MPI tasks does neither affect the order in which the samples are stored nor the order in which the samples are loaded again. To convince yourself, here are two code snippets:
Save a sample list:
```
import nifty8 as ift
from mpi4py import MPI
comm = MPI.COMM_WORLD
n_tasks = comm.Get_size()
my_rank = comm.Get_rank()
master = my_rank == 0
n_samples = 5
sp = ift.RGSpace(1)
mean = ift.full(sp, 0)
# create samples with "value of sample=index in list"
# create samples mpi parallel according to nifty convention
loc_inds = ift.utilities.shareRange(n_samples, n_tasks, my_rank)
smps = [ift.full(sp, ii) for ii in range(*loc_inds)]
neg = [False for _ in range(*loc_inds)]
samples = ift.ResidualSampleList(mean, smps, neg, comm)
samples.save('smp')
if master:
print(f'saved sample list with {n_samples} samples distributed on {n_tasks} tasks')
```
Read the sample list and verify the number of samples and their order:
```
import nifty8 as ift
from mpi4py import MPI
comm = MPI.COMM_WORLD
n_tasks = comm.Get_size()
my_rank = comm.Get_rank()
master = my_rank == 0
samples = ift.ResidualSampleList.load('smp', comm)
n_samples = samples.n_samples
# check order of samples
for ii, smp in enumerate(samples.iterator()):
assert(ii == smp.val[0])
if master:
print(f'read sample list with {n_samples} samples, and distribute on {n_tasks} tasks')
print('verified order of samples')
```
Thanks for noticing this Maximilian!https://gitlab.mpcdf.mpg.de/ift/nifty/-/merge_requests/835Sampling: Do not raise on not converged samples2023-01-13T11:59:35ZGordian EdenhoferSampling: Do not raise on not converged samplesGordian EdenhoferGordian Edenhofer