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@bjoernenders bjoernenders released this 09 Oct 02:03
· 355 commits to master since this release
v0.3.0
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PtyPy 0.3 release notes

We are happy to announce that ptypy 0.3 is now out. If you have been using the ptypy 0.2 (from the master branch), the transition should be smooth but far from automatic - see below. The essence of this new release is

  1. a redesign of ptypy's internal structure, especially the introduction of an extendable ScanModel, which should make new ideas and new algorithms easier to implement (a big collective effort involving A. Björling, A. Parsons, B. Enders and P. Thibault),

  2. support for 3D Bragg ptychography, which uses the new ScanModel structure (all thanks to A. Björling),

  3. extensive testing of most components of the code, and Travis CI integration (huge work by A. Parsons and important contributions by S. Chalkidis),

  4. more dimensions for Storage classes, reduced memory footprint and reduced object count, as Views are now slotted and don't hold other objects (B. Enders and A. Björling), and

  5. the introduction of the descriptor submodule, which manages the whole parameter tree, including validation, defaults, and documentation (collective effort led by B. Enders and P. Thibault)

Breaking changes

The streamlining of the input parameters means that all reconstruction scripts for version 0.2 will now fail. We had no choice.

The changes were required in order to solve the following problems:

  1. Parameter definitions, documentations and defaults were in different locations, so hard to track and maintain
  2. The meaning of a branch set to None was ambiguous.
  3. Basic experiment geometry (some distances, radiation energy, etc) could be specified at two different locations.
  4. In general, the standards were not clear.

The solution to all these problems came with the descriptor submodule. For a user, what matters most is that ptypy.defaults_tree now contains the description of the full set of parameters known to ptypy.

defaults_tree

Here's a short example of how defaults_tree is used internally, and how you can used it in your scripts or on the command line to inspect ptypy's parameter structure.

import ptypy

# Extract one branch
desc_DM_simple = ptypy.defaults_tree['engine.DM_simple']

# Print out the description of all sub-parameters
print desc_DM_simple.to_string()
[numiter]
lowlim = 1
help = Total number of iterations
default = 123
type = int

[numiter_contiguous]
lowlim = 1
help = Number of iterations without interruption
default = 1
doc = The engine will not return control to the caller until this number of iterations is completed (not processing server requests, I/O operations, ...).
type = int

[probe_support]
lowlim = 0.0
help = Valid probe area as fraction of the probe frame
default = 0.7
doc = Defines a circular area centered on the probe frame, in which the probe is allowed to be nonzero.
type = float

[name]
help = 
default = DM_simple
doc = 
type = str

[alpha]
lowlim = 0.0
help = Difference map parameter
default = 1
type = float

[overlap_converge_factor]
lowlim = 0.0
help = Threshold for interruption of the inner overlap loop
default = 0.05
doc = The inner overlap loop refines the probe and the object simultaneously. This loop is escaped as soon as the overall change in probe, relative to the first iteration, is less than this value.
type = float

[overlap_max_iterations]
lowlim = 1
help = Maximum of iterations for the overlap constraint inner loop
default = 10
type = int

# Generate defaults
p = desc_DM_simple.make_default(depth=1)

# Validate
# (try with ptypy.utils.verbose.set_level(5) to get detailed DEBUG output)
desc_DM_simple.validate(p)

# Here's what happens if a parameter is wrong:
p.numiter = 'a'
desc_DM_simple.validate(p)
ERROR root - numiter                                            type                 INVALID
(...)

How reconstruction scripts have to be changed

  1. All scans sub-entry have a name. This name is one of the ScanModel classes, for now only Vanilla, Full, and Bragg3dModel. Most users will want to use Full. Others will come as we implement engines that require fundamental changes in the pod creation.

  2. Data preparation: the sub-tree recipe does not exist anymore, and all parameters associated to a PtyScan subclass are specified directly in the scan.???.data sub-tree. The geometry sub-tree is also gone, with all relevant parameters also in the scan.???.data sub-tree.

  3. There is no more an .engine sub-tree. This used to be present to change the default parameters of specific engines (or all of them using engine.common) before engines are declared in the engines.* sub-tree. We have found that this duplication is a source of confusion. Now the single place where engine parameters are set are within the engines.* sub-tree.

  4. A sub-tree cannot be set to None. To deactivate a feature associated to a sub-tree, one has to set active=False. For instance io.autoplot = None is not valid anymore, and io.autoplot.active = False has to be used instead.

Other contributions

  • Option to use pyfftw (thanks to L. Bloch, ESRF)
  • Scalability tests (thanks to C. Kewish, Australian Synchrotron)
  • A first draft jupyter-based plot client (B. Daurer, now National University of Singapore)
  • Bug fixes and tests (many people)

Roadmap

The next release will focus on optimisation and speed. We will also soon switch to python 3.

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