-
imagetool: reimplement axis linking logic (8f8648c)
Limits for all axes that correspond to the same dimension are now shared.
Furthermore, view limits are now also shared across linked tools.
-
io.dataloader: display progress bar when loading data from multiple files (#91) (4d3a704)
A progress bar is now displayed by default when loading data that spans multiple files. The visibility of the progress bar can be controlled with the newly added
progress
argument toerlab.io.load
.
-
imagetool.manager: ensure compatibility with lazy-loaded data (6d57e13)
-
analysis.gold: fix incorrect normalization for Fermi edge fits and add resolution parameter (1fe773d)
-
analysis.fit.functions.general: properly normalize convolution kernel for small sigma (390769e)
-
ktool: resolve incompatibility with hv-dependent data (#88) (472e98e)
- analysis.fit.models.FermiEdgeModel: micro-optimizations related to EF guessing (afc5c90)
-
goldtool: add initial resolution spinbox (9d8dd8d)
-
analysis.gold.quick_fit: enable resolution plot customization through keyword arguments (a3058e6)
-
io.plugins.da30: support loading unzipped DA30 scans (#89) (eadc676)
-
explorer: add a new interactive tool for browsing file systems (a70b222)
Adds a
explorer
GUI window that provides a view of the file system with a summary of selected ARPES data files.The window can be started within ImageTool Manager from the File menu, or as a standalone application with
python -m erlab.interactive.explorer
.Closes #83.
-
misc: add function to open directory in system's file manager (7d3db3f)
-
io.exampledata: replace
sph_harm
deprecated in scipy 1.15.0 withsph_harm_y
(eba902c) -
interactive.utils: ignore all other arguments for separator actions in
DictMenuBar
(5c94b92)This fixes unintended text showing alongside menubar separators in some operating systems.
-
imagetool.manager: fix archived files being deleted after a few days (7d93442)
-
io.exampledata: update sph_harm usage to match scipy 1.15.0 changes (1dde195)
-
replace direct
typing
imports with namespace imports (fc2825d) -
imagetool: update type hints and preload fastbinning module (ab0b3fd)
-
io: improve docs structure by reorganizing namespace (5e2d7e5)
-
io: improve error messages for folders (8d63c09)
-
restool: improve parameter guessing and copied code formatting (0b33770)
The temperature and center can now be guessed independently.
-
plotting: add
literal
option for point label formatting inmark_points_outside
, consistent withmark_points
(db723fd) -
generalize fomatting DataArray to raw HTML (85c735e)
-
analysis.gold: add plot capability to
quick_fit
and deprecate quick_resolution (903450b)Future code shoule use
quick_fit
withplot=True
instead ofquick_resolution
. -
ktool: add work function spinbox (31c5ae8)
-
io.dataloader: adds a
extensions
attribute to data loaders (a819960)Data loaders can now choose to implement an
extensions
attribute that returns a set of file extensions supported by the loader. This reduces the possibility of the user trying to load files with a wrong loader and gives informative error messages. -
io: expose
load_krax
as public API (3508a0a)Adds a new function
erlab.io.utils.load_krax
that can parse MBS deflector maps saved as.krx
.
-
imagetool.manager: implement threaded file loading (feeb06b)
Data are now loaded in the background.
-
plotting: properly expose
__all__
(03cdf89) -
imagetool: inverted state and aspect ratio of axes are now properly restored (321c837)
- imagetool: make imagetool respect the most recently used loader and data directory if opened in the manager (df1d550)
-
introduce
utils.array.sort_coord_order
function (0e694d2)Sorts coordinates order to be prettier! Sorting now applied in various places such as data loaders, ImageTool, and the
qsel
accessor. -
interactive: add
restool
(fd838b1)Adds a new interactive tool
restool
for fitting Fermi-Dirac distributions with a linear background to EDCs averaged over angles. The angle and energy range can be adjusted interactively. -
imagetool.manager: add integration with IPython (cf346b9)
Adds a new action that stores data with the
%store
magic command. With this, it is much more easy to import data processed in the manager into jupyter notebook sessions. -
imagetool.manager: add preview (9fdc63d)
Adds an image preview panel that shows the main image of the selected data.
Also, a new hover preview option can be toggled on to show the preview images when hovering over each item.
-
kspace: properly handle maps with energy given as kinetic (02bce90)
-
io.plugins.erpes: show warning when loading with index is ambiguous (95a88b6)
-
io: fixes loaded data losing their original names (a19f37a)
-
analysis.fit: handle NaN values in linear fit guesses (1aef937)
-
imagetool.manager: fix undefined selection order (4c486e2)
- improve import time (e2a2542)
-
reorganize interactive module structure (87a6e89)
-
imagetool: add
update
parameter toapply_func
(fd0238d) -
accessors.kspace: make errors during momentum conversion due to missing coords or attrs more explicit (eb3d01c)
-
imagetool: change argument
use_manager
tomanager
initool()
(0929e5c) -
imagetool: move main window setup from
__init__.py
tomainwindow.py
(0997149)This refactor enhances maintainability and readability by clearly separating the main window setup logic from the package initialization.
-
imagetool: disable manager by default (34e943f)
This update modifies
itool
andqshow
so that tools are opened in the manager only whenuse_manager=True
is explicitly specified.To address the inconvenience, a new
Move to Manager
action with keyboard shortcutCtrl+Shift+M
has been added to theFile
menu of ImageTool windows opened outside the manager when the manager is running. -
make sequence type checking function public and move to
utils
module (0475cfd)Adds
utils.misc.is_sequence_of
, which checks if an object is a sequence of elements of the specified type. -
imagetool: show all axes by default for 4D data (b034477)
-
imagetool: add icons to context menu items that opens a new window (1f548f7)
-
imagetool: streamline window title naming (0f9dcda)
-
replace boilerplate decimal calculation with new
utils.array.effective_decimals
(7873669) -
imagetool: initial migration to QAction (7807174)
Mostly internal changes that reduces duplicate code and makes keyboard shortcuts robust.
-
imagetool.manager: refactor console and jitted functions to private modules to improve startup time (280bfd8)
-
io: improve loader registry repr with descriptions and dynamic formatting (3f43405)
-
io: add descriptions to loaders for better user guidance (7087c04)
-
dtool: add boxcar filter and 1D curvature, along with internal improvements (0bd2b17)
-
analysis.image: add
diffn
function for nth derivative calculation (a70812f)Adds a function that calculates accurate n-th order partial derivatives of DataArrays using findiff.
Also, functions that use derivatives including
curvature
andscaled_laplace
now uses properly scaled derivatives from findiff. As a consequence, the output of these functions may be slightly different. -
analysis.image: add boxcar filter (7475266)
-
analysis.image: add 1D curvature (522d554)
-
io.plugins.erpes: add data loader for our homelab system! (48dcbb4)
-
io.plugins.merlin: allow loading BL4 single file in
ImageTool
file menu (079914e) -
io.dataloader: automatically load in parallel with per-loader threshold (33a8c63)
-
imagetool: add support for DataTree objects (c4c03e3)
-
imagetool.manager: fix dark mode handling and focus management in console (ed81f70)
-
imagetool.manager: bind associated tools to the manager (a38cf7f)
With this change, closing an ImageTool window no longer affects tools such as ktool and dtool opened in that ImageTool.
-
imagetool: make dimension order in exported image data from image plot consistent with the GUI (0ee225b)
-
imagetool: fix issue with selection with multiple binned dimensions (121c968)
-
io.dataloader: adjust condition to handle single file loading (d98c71f)
-
io.plugins.da30: update
DA30Loader
to handle multiple regions in one.pxt
file (1ff8b93)
-
io: deprecate choosing loaders with their aliases, closes #76 (464ee45)
-
interactive.utils: improve code generation (2b24e08)
-
replace direct imports with module references (b3ca55c)
-
io.nexusutils: defer error message until actually trying to load nexus files (8eec5aa)
-
enforce strict monotonicity check in data loader (513554e)
-
da30: return empty dict instead of None for matches in loader (2d8b8ae)
-
io.dataloader: assign coords also for multifile scan of length 1 (0b14f75)
-
io.plugins.merlin: adjust handling logic for motor scan aborted after one file (1ac25f1)
- io: implement lazy loading (da5244a)
- update deprecation warnings to FutureWarning for improved clarity (f2d7ae7)
- docs: ensure docstring compatibility with matplotlib 3.10.0 (e881a6b)
-
io.dataloader: enhance data combination logic (80f2772)
When given multi-file data with multiple coordinates, the previous behavior was to include every coordinate as a dimension. This is logical for scans such as 4D position-dependent scans, but unnecessary for data like hv and angle dependent scans. Now, the loader will concatenate only along one axis if all motor coordinates are strictly monotonic.
-
constants: add Bohr radius (f8e4ca2)
-
imagetool.manager: enable concatenating selected data (44d61ba)
-
imagetool: add normalization option for 1D plot data (5417a32)
Adds an option to normalize 1D data with its mean to the right-click menu of 1D plots.
-
add lazy-loader support (e5ec658)
Properly implements SPEC 1 lazy-loading to top-level modules and the analysis module. Users can now directly access submodules after importing the top-level module only:
import erlab erlab.analysis.transform.rotate(...)
-
imagetool.manager: add console (470808f)
Adds a python console to the manager that can be triggered from the
View
menu. -
imagetool: add keyboard shortcut to close ImageTool window (97a7533)
-
interactive.imagetool: add info box to manager (0918a5b)
Adds a textbox to ImageTool manager that shows coordinates and attributes of the selected window.
-
kspace: fix broken hv-dependent data momentum conversion (4695583)
Fixes completely wrong implementation of kz-dependent momentum conversion. I can't believe this went unnoticed!
-
imagetool: remove and reapply filter upon transformation (af54a1d)
-
imagetool: fix nonuniform data io and cropping (8b538e6)
-
imagetool: fix wrong cursor position when loading ImageTool state from file (e8191a8)
-
imagetool: resolve menu widgets losing keyboard focus (90f8868)
-
imagetool.manager: accelerate opening new windows within the manager (d4380b7)
-
delay imports for performance optimization in interactive tools (abac874)
-
plotting: update import statements to use
erlab.plotting
directly and deprecateerlab.plotting.erplot
(6a19f6a)The import convention
import erlab.plotting.erplot as eplt
is now deprecated. Users should replace them withimport erlab.plotting as eplt
. -
imagetool: streamline namespace handling and improve layout structure (5506f18)
-
imagetool: move center zero button to context menu (48deb6d)
-
improve cli interface (34a4db1)
-
cleanup some function signatures (b04df05)
-
analysis.fit: enable lazy loading for fit functions (e877e12)
-
imagetool.manager: add ipython-based console (f0b0adf)
-
analysis.gold: adjust resolution plot cosmetics (5d4a486)
-
interactive.colors: minimize number of default colormaps (a4c750c)
Reduces the number of colormaps initially available in ImageTool. All colormaps can be loaded from the right-click menu of the colormap selection widget.
-
interactive.imagetool: simplify method names for clarity (48d0453)
-
plotting: correct axis labels in
plot_array_2d
(2fa358a) -
interactive.imagetool: fix selection and io for non-uniform data (5670a15)
-
accessors.kspace: fix binding energy detection (ed26162)
-
interactive.imagetool: show unarchiving message on double click (d3dd3ee)
-
interactive.imagetool: fix saving and loading non-uniform data (73a1d4b)
- interactive.imagetool: fix compatibility issues with Windows (8691014)
-
interactive.imagetool: overhaul manager UI (a2ce551)
Replaced widget-based implemenation with a model/view architecture. As a consequence, the displayed interface looks like a list. The user can now click a selected item to rename it, and drag items to reorder them. Each item now has a dedicated right-click menu.
-
interactive.imagetool.manager: improve file opening (da3425f)
Implements opening multiple files at once through the open menu of the manager. Also, add support for opening data files by dragging them into the manager window.
-
interactive.imagetool: add save and load functionality for workspace (a5d38af)
Enables users to save multiple ImageTool windows to a single file using the manager.
-
interactive.imagetool: show dialog when data is being loaded (5577249)
-
interactive.imagetool: change manager icon (3e20e63)
-
interactive.imagetool.manager: add menubar to manager (59326a1)
-
io.plugins: add summary generation to maestro loader (aa6f5d2)
-
plotting: add fine-grained control over color limit normalization (46c962f)
-
interactive.imagetool: open ktool from imagetool (d2cb8a7)
-
interactive.imagetool: add equal aspect ratio checkbox to right-click menu (d4db0cf)
-
interactive.imagetool: add crop menu (639749f)
-
interactive.utils: add qobject that handles mutually exclusive selection comboboxes (33b5f6b)
-
interactive.imagetool: add rename button to manager (56ac884)
-
interactive.imagetool: add open in new window option to right-click menu of each plot (8742659)
-
accessors.general: added
qshow.params
accessors for fit results (2592e5a)Calling
ds.qshow.params()
on a fit result dataset will now plot the coefficient value and errorbars as a function of fit coordinates. -
analysis.fit: add Fermi-Dirac distribution to MultiPeakFunction components (65a1e8c)
-
io.dataloader: add itool button to interactive summary (ba3aa15)
A button that can open the data directly in ImageTool has been added to the interactive summary. The button is displayed when the interactive summary is called while the ImageTool manager is running.
-
io.plugins.lorea: fix file dialog method (4c74105)
-
interactive.imagetool: resolve segfault on save current data (5699fa3)
-
interactive.imagetool: retain axis order when opening dtool and goldtool (e14c9fc)
-
io.plugins.merlin: fix match signature (5586cce)
-
interactive.imagetool: cursor sync for non-uniform coords (4aa1425)
-
io.plugins.maestro: fix wrong temperature attribute (6ed2a70)
-
io.dataloader: allow dimensions without coordinates in output data (752facf)
-
interactive: improve ktool compatibility with manager (4c775cf)
-
interactive.imagetool: fix opening slice in new tool when manager is running (db8e0af)
-
interactive.utils: fix opening with manager in tools (3726049)
-
accessors.general: allow
qshow
for fit results from multivariable Datasets (f5b88e7) -
interactive.imagetool: fix wrong decimals for rotation center (3fc3a50)
-
accessors.general: fix component plotting for concatenated fit datasets with multiple models (7d2976d)
-
interactive.imagetool: improve associated tool garbage collection (839dab0)
-
io: implement lazy loading for h5netcdf and nexusformat imports (3f219ae)
-
speed up initial import (d7f3b3c)
Accelerates initial import time by refactoring heavy imports to reside inside functions.
Importing the plotting module no longer automatically imports the colormap packages
cmocean
,cmasher
, andcolorcet
. The user must add manual import statements. -
analysis.interpolate: cache jitted interpolation functions (34521ef)
-
interactive.imagetool: optimize memory usage by reducing circular references (a675e1a)
-
interactive.imagetool: make it easier to show and hide windows in manager (aefc560)
-
interactive.imagetool: use
QSharedMemory
instead ofmultiprocessing
(234c19f) -
plotting.general: use matplotlib api instead of xarray plot for 1D (9e38b2c)
-
io.dataloader: improve warning messages and error handling (1ebfa72)
-
interactive: move IconButton to interactive utils and add IconActionButton (e78190f)
-
interactive.imagetool: use HDF5 files instead of pickle to cache tools (be66297)
-
move
AxesConfiguration
fromerlab.analysis.kspace
toerlab.constants
(3593d41) -
plotting: streamline igor CT loading (e1e8baa)
-
io: update type hints for file handling functions to use Iterable (e3caf83)
-
io: streamline file identification logic and add user warnings for multiple file scenarios (05b7e6c)
-
io: replace several
os.path
calls with pathlib (bdfdd22) -
dataloader: make some methods private (31cf008)
This makes all dataloader methods and attributes that are not meant to be overriden private. Affected methods and properties are
combine_multiple
,generate_summary
, andname_map_reversed
. -
accessors.kspace: cleanup namespace (7af0d66)
Withdraws some internal properties and methods from public API.
-
directly import
_THIS_ARRAY
from xarray core (3bd72ec) -
interactive.imagetool: improve dialog code structure (5a16686)
-
interactive.imagetool: move dialogs into new dedicated module (a90a735)
-
interactive.imagetool: improve error messages for invalid data (a715ba1)
-
Deprecated module
erlab.io.utilities
is removed. Useerlab.io.utils
instead. (e189722) -
Deprecated module
erlab.interactive.utilities
is removed. Useerlab.interactive.utils
instead. (af2c81c) -
Deprecated module
erlab.characterization
is removed. Useerlab.io.characterization
instead. (8d770bf) -
Deprecated module
erlab.analysis.utils
is removed. Useerlab.analysis.transform.shift
anderlab.analysis.gold.correct_with_edge
. (0b2ca44) -
Deprecated alias
slice_along_path
inerlab.analysis
is removed. Call fromerlab.analysis.interpolate
instead. (305832b) -
Deprecated aliases
correct_with_edge
andquick_resolution
inerlab.analysis
are removed. Call fromerlab.analysis.gold
instead. (075eaf8) -
Removed deprecated aliases
load_igor_ibw
andload_igor_pxp
. Usexarray.open_dataarray
andxarray.open_dataset
instead. (7f07ad2) -
The default attribute name for the sample temperature is changed to
sample_temp
fromtemp_sample
. This will unfortunately break a lot of code that relies on the keytemp_sample
, but will be easy to refactor with find and replace. (32e1cd5) -
All dataloaders must now add a new keyword argument to
load_single
, but implementing it is not mandatory.Also, dataloaders that implements summary generation by overriding
generate_summary
must now switch to the new method.See the summary generation section in the updated user guide.
Furthermore, the
isummarize
method is no longer public; code that uses this method should usesummarize
instead.The
usecache
argument to thesummarize
method is no longer available, and the cache will be updated whenever it is outdated. (0f5dab4)
-
io.igor: enable loading experiment files to DataTree (1835be0)
Added methods to the backend to allow using
xarray.open_datatree
andxarray.open_groups
with Igor packed experiment files. Closes #29 -
add
qinfo
accessor (eb3a742)Adds a
qinfo
accessor that prints a table summarizing the data in a human readable format. Closes #27 -
interactive.kspace: pass lattice parameters and colormap info to
ktool
(6830af3)Added the ability to pass lattice vectors and colormaps to
ktool
. -
interactive.kspace: add circle ROI to ktool (304e1a5)
Added a button to the visualization tab which creates a circle ROI. The position and radius can be edited by right-clicking on the roi.
-
interactive.colors: add zero center button to right-click colorbar (c037de1)
-
interactive.imagetool: add
.ibw
and.pxt
files to load menu (73c3afe) -
io.dataloader: allow passing rcParams to interactive summary plot (a348366)
-
io.dataloader: implement automatic summary generation (0f5dab4)
It is now much easier to implement a summary generation mechanism. This commit also adds a new keyword argument to
load_single
that can greatly speed up summary generation. -
io.dataloader: support callable objects in
additional_attrs
(e209499)
-
interactive.imagetool: fix copy cursor value for numpy 2 (dc19c82)
-
io.dataloader: retain selected dimension in interactive summary (9d54f8b)
-
accessors.general: keep associated coords in
qsel
when averaging (03a7b4a) -
io.dataloader: ignore old summary files (bda95fc)
-
io.plugins.kriss: fix KRISS ibw file match pattern (7ced571)
-
analysis.gold: retain attributes in
quick_resolution
(504acdc) -
do not require qt libs on initial import (118ead6)
-
io.plugins.da30: faster summary generation for DA30 zip files (22b77bf)
-
io.igor: suppress
igor2
logging (5cd3a8c) -
analysis.interpolate: extend acceleration (84daa88)
The fast linear interpolator now allows more general interpolation points like interpolating 3D data on a 2D grid. This means that passing
method='linearfast'
toDataArray.interp
is faster in many cases.
-
io.igor: change wave dimension name handling (3e0586a)
Waves with both dim and unit labels provided were given a dim label formatted like
dim(unit)
. This update changes this so that the dim label is justdim
, and the unit is inserted to coordinate attrs. -
io: remove deprecated module (e189722)
-
interactive: remove deprecated module (af2c81c)
-
remove deprecated module
erlab.characterization
(8d770bf) -
analysis: remove deprecated module (0b2ca44)
-
analysis: remove deprecated alias (305832b)
-
analysis: remove deprecated aliases (075eaf8)
-
interactive.imagetool.manager: add prefix to temporary directories for better identification (e56163b)
-
io.plugins: implement DA30 file identification patterns in superclass (f6dfc44)
-
io: remove deprecated aliases (7f07ad2)
-
change temperature attribute name (32e1cd5)
Changes
temp_sample
tosample_temp
for all data loaders and analysis code. -
utils.formatting: change formatting for numpy arrays (95d9f0b)
For arrays with 2 or more dimensions upon squeezing, only the minimum and maximum values are shown. Also, arrays with only two entries are displayed as a list.
-
io.dataloader: disable parallel loading by default (fed2428)
Parallel loading is now disabled by default since the overhead is larger than the performance gain in most cases.
-
change some warnings to emit from user level (e81f2b1)
-
io.dataloader: cache summary only if directory is writable (85bcb80)
-
io.plugins: improve warning message when a plugin fails to load (9ee0b90)
-
io: update datatree to use public api (6c27e07)
Also bumps the minimum supported xarray version to 2024.10.0.
-
io.dataloader: make
RegistryBase
private (df7079e) -
io.dataloader: rename loader registry attribute
default_data_dir
tocurrent_data_dir
(d87eba7)The attribute
default_data_dir
has been renamed tocurrent_data_dir
so that it is consistent withcurrent_loader
. Accessing the old name is now deprecated.Also, the
current_loader
andcurrent_data_dir
can now be assigned directly with a syntax likeerlab.io.loaders.current_loader = "merlin"
.
-
interactive.imagetool: add normalization option to View menu (53e2cf2)
-
io.dataloader: allow passing additional arguments to
load_single
(1652c20) -
io.plugins: add support for two new beamlines, closes #61 (368263e)
Added plugins with preliminary support for Diamond I05 and ALBA BL20 LOREA.
-
io: add
nexusutils
module for working with NeXus files (2532941)This commit adds a new submodule
io.nexusutils
that contains utilities for converting NeXus data to xarray data structures.
-
erlab.io.plugins.merlin: resolve typo in file dialog methods (39caa99)
-
erlab.accessors.general: make
qsel
accessor work along dimensions with no coordinates (7f0d259) -
interactive.imagetool: avoid errors on termination (9fd044b)
- io: return path-like objects instead of strings in
get_files
(2eb9166)
- io.dataloader: fix
coordinate_attrs
not being propagated (278675b)
- add app icon for imagetool manager (e1cbcd2)
-
io.dataloader: add new argument that can control combining (bdec5ff)
Adds a new parameter
combine
toio.load
. IfFalse
, returns a list of post-processed files without attempting to concatenate or merge the data into a single object. IfTrue
, retains the current default behavior.
-
imagetool: allow coords of any dtype coercible to float64 (4342ebc)
-
io.dataloader: properly handle combining multi-axis scans (2cd22c7)
-
io.plugins: update type hints (54d0c5d)
-
remove unused imports (f1e35de)
-
interactive: add informative error message for missing pyqt (1347a02)
-
io.plugins: add warning when plugin load fails (ed5b184)
-
io.plugins: add loader for beamline ID21 ESM at NSLS-II (c07e490)
This commit adds a new data loader for beamline ID21 ESM at NSLS-II, Brookhaven National Laboratory.
-
io.dataloader: add formatters (2ee9a4a)
A new attribute named
formatters
and a new methodget_formatted_attr_or_coord
has been added to loaders. This allows custom per-attribute pretty-printing behavior. -
io: add parallel argument to
load
(88cd924) -
io: add xarray backend for igor files (1fe5ca5)
.pxt
,.pxp
, and.ibw
files can now be opened with xarray methods such asxr.open_dataset
andxr.open_dataarray
. See the updated user guide for more information.
-
io.dataloader: properly reorder coordinates (3ebfb0f)
Coordinate order was broken for loaders which assign coordinates in inherited
post_process
. This is now fixed, and returned data will be consistently ordered with respect to the mapping, with the dimension coordinates coming first. -
erlab.io.plugins.maestro: temporary fix for xarray issue (c2d04a3)
-
io.plugins.da30: properly handle output types (6297aba)
The DA30 loader now tries to return a dataset from
.zip
files only when there are no coordinate conflicts. In the case of conflicts, the loader will return aDataTree
.Also, single region DA30
.pxt
files will now return aDataArray
consistent with the equivalent.ibw
file. -
interactive.fermiedge: allow transposed input to fermi edge fitting tool (dcae75e)
-
interactive.imagetool: retain attrs when exporting slice (1bed572)
When accessing the data of a single slice from the right-click menu of
ImageTool
, the attributes of the original data are now kept. This allows saved slices or data opened in other tools to retain their attributes. -
resolve gui script not working on windows with conda (62253d0)
-
io.dataloader: clear plot before loading in interactive summaries (21d6dea)
-
plotting.general: fix
plot_slices
compatibility with slice object as argument (5948a7b) -
io: disable memmapping when loading data (c39da1b)
Memmapping seemed to interfere loading multiple files when called through ipywidgets.
- interactive.imagetool: improve manager speed (891c4ee)
-
io.utils: use pathlib in
get_files
(b7a0f5b) -
io.plugins.merlin: combine ImageTool file menu into single entry (6e28ac2)
-
io: add postprocessing and validation for
DataTree
objects (3fb3ff5) -
io: add warning when file is ambiguous (8daabb8)
-
io: remove renaming steps from
load_single
in multi-file loaders (542f4f2)Combining before renaming coords should be more straightforward
-
io: allow missing alpha coord (c9deed4)
Validation checks will not warn about missing detector angle, allowing XPS measurements.
-
io.dataloader: only allow real file or folder names as input (b9a59cc)
The previous behavior allowed passing
f_001.pxt
to loadf_001_S001.pxt
,f_001_S002.pxt
... but this was confusing since there is no file namedf_001.pxt
. This commit disallows such input. -
cleanup erplot namespace (007eedb)
-
io: implement metaclass (e787b1c)
Whenever the
identify()
method failed to find any files, subclasses had to explicitly raiseFileNotFoundError
. This resulted in a lot of boilerplate code and ambiguous error messages. Now, all subclasses can just returnNone
inidentify()
when no files are found. The appropriate error is automatically raised. -
io.igor: raise OSError on load fail (6c7a4c4)
-
move dataloader cell formatting implementation to utils module (0f2cb1c)
-
io: deprecate calling igor functions from top level namespace (bb8af7c)
Calling
erlab.io.load_wave
anderlab.io.load_experiment
is deprecated. When writing new code, usexarray.load_dataarray
andxarray.load_dataset
instead.
- ui file compatibility with Qt5 (66c776d)
-
interactive.imagetool: add rotation (fdeb8a9)
A rotation dialog has been added to the Edit menu. Rotation guidelines can be overlaid on the main image.
-
interactive.utils: add rotatable lines that can be rotated by dragging (31b55e5)
-
analysis.transform: add
rotate
function (83a2ad8)Added a new function that can rotate DataArray values using spline interpolation. Previous simple implementations are marked as deprecated.
-
utils.array: add new function
trim_na
(c628b5b)This function trims the edges of DataArrays where all values are NaN.
-
accessors.kspace: add method argument (204073e)
Momentum conversion through the
convert()
method of the kspace accessor now supports an additional keyword argumentmethod
that can be used to choose different interpolation methods supported byscipy.interpolate.RegularGridInterpolator
. Note that methods other than'linear'
will take much longer to execute. -
analysis.interpolate: add solver args (24be3b0)
FastInterpolator
now supportssolver
andsolver_args
keyword arguments introduced in scipy 1.13.0. -
interactive.colors: implement
BetterColorBarItem
limit editor (7dd1477)A new context menu in
BetterColorBarItem
's viewbox enables manually editing color limits. -
analysis.interpolate: implement slicing along a vector (cba8567)
A new function
slice_along_vector
has been added which enables interpolating through a line defined by a vector and a point. -
interactive.imagetool: add goldtool and dtool to menu (33d5e35)
The interactive tools goldtool and dtool are now directly accessible from the right-click menu of 2D images in ImageTool.
-
accessors.general: add option to
qsel.around
to disable averaging (5aaed85) -
plotting.general: add
NonUniformImage
functionality toplot_array
(86d8c1a)plot_array
can now plot data with unevenly spaced coordinates. It usesmatplotlib.image.NonUniformImage
with the default interpolation option set to 'nearest'. The resulting plot may be different fromxarray.DataArray.plot
which usespcolormesh
to generate image plots. -
interactive.imagetool: add copy limits to colorbar menu (29c37c4)
Right-clicking on the colorbar will now show a menu which contains a button that copies the current color limits to the clipboard. This is useful when manually adjusting color limits.
-
interactive.imagetool: properly disconnect signals (dce236f)
-
interactive.imagetool: fix autoscale when loading data (2c12f59)
-
interactive.imagetool: scale spinbox decimals relative to coordinate step size (9a801a5)
-
interactive.utils: update
BetterSpinBox
width on changing decimals (0a70884) -
interactive: fix compatibility issue with PySide6 (da5f4af)
-
interactive.imagetool: do not copy code when unnecessary (9131029)
-
accessors.general: qshow now triggers hvplot properly for 1D data (8a84813)
-
interactive.imagetool: make manager socket use default backlog (0ac7f0b)
-
interactive.imagetool: ensure proper socket termination in manager (2cceb27)
-
interactive.utils: improve code generation (78c403f)
-
analysis: move
shift
totransform
(08baf05)The
shift
function has been moved fromutils
totransform
. Calling from theutils
module is now deprecated. -
analysis: cleanup namespace (e3e641d)
Three functions that were directly accesible from the
erlab.analysis
namespace are now deprecated. Import them from their respective modules. -
remove deprecated module
analysis.utilities
(8b79ab5) -
analysis.image: add check for NaN in input (095554f)
Derivative functions now check for NaNs in input data and raise a warning.
The interactive derivative tool automatically fills NaNs in the input data with zeros and shows a warning message.
-
remove unpacking inside
np.r_
(6c27864) -
improve initial import time (f720973)
-
plotting.annotations: properly pass keyword arguments in
mark_points_outside
(2136939) -
plotting.annotations: expose property label generation to public api (545781d)
A new
property_labels
function can be used to generate strings that are used bylabel_subplot_properties
so that the labels can be used as titles easily througheplt.set_titles
. Also, label generation now recognizes time, given as 't' with default unit seconds.
-
erlab.plotting.general: improve
plot_array
keyword versatility (1dc41cd)Enables additional kwargs with valid data dimensions as the key to be passed onto
qsel
. -
erlab.analysis.gold: fix
quick_fit
attribute detection (3797f93) -
interactive.imagetool: retain window title upon archiving (b5d8aa4)
-
plotting.general: remove
LabeledCursor
(912b4fb)We skip the deprecation step since nobody is likely to be using it anyway.
-
accessors: split submodule (6ed5c03)
Accessors in
utils.py
has been moved togeneral.py
, so thatutils.py
only contains utilities for creating accessors. -
improve type annotations (b242f44)
-
interactive.imagetool: various fixes related to manager (3d3f55e)
This fix incorporates many changes to the ImageTool and ImageTool Manager.
First, the archiving function of the manager now works properly, and tries to clear memory eagerly.
When opening data from a file using the GUI, the name of the file will now be displayed in the title bar of the ImageTool. This file name is also propagated to the name displayed in the manager.
Furthermore, the archiving and show/hide functionality of the manager has been updated to restore the window geometry automatically. When the user shows or unarchives a hidden or archived window, the previous position of the window is restored.
Some icons and the layout of the manager has been modified, and tooltips has been added to the buttons.
Also, some unexpected behavior regarding linking has been resolved.
-
plotting.plot3d: temporarily disable broken monkey patch (220f23f)
-
replace broken signature for dynamic functions (39a3954)
-
interactive.imagetool: fix broken binning controls on loading fron GUI (0ca5437)
-
interactive.imagetool: fix crash while linking more than 3 tools (d5f8a30)
-
update resistance loader (6fcf2ab)
- interactive.imagetool: show error message in GUI when opening file (287a7e8)
-
interactive.imagetool: properly implement caching and linking from GUI (ffacdce)
-
plotting.general: pass DataArray to
func
argument toplot_array
(ed76e64)
-
interactive.imagetool: speedup file loading and saving (a6c869b)
Use pickle to save and load files instead of
erlab.io.load_hdf5
anderlab.io.save_as_hdf5
.
-
erlab.io.plugins.ssrl52: changes to loader (512a89b)
The loader now promotes all attributes that varies during the scan to coordinates. Also, if the energy axis is given in kinetic energy and the work function is inferrable from the data attributes, the energy values are automatically converted to binding energy. This may require changes to existing code. This commit also includes a fix for hv-dependent swept cuts.
-
erlab.io.dataloader: reorder output coordinates (178edd2)
Coordinates on the loaded data will now respect the order given in
name_map
andadditional_coords
, improving readability. -
interactive.imagetool: add ImageTool window manager (b52d249)
Start the manager with the cli command
itool-manager
. While running, all calls toerlab.interactive.imagetool.itool
will make the ImageTool open in a separate process. The behavior can be controlled with a new keyword argument,use_manager
. -
interactive.imagetool: add undo and redo (e7e8213)
Adjustments made in ImageTool can now be undone with Ctrl+Z. Virtually all actions except window size change and splitter position change should be undoable. Up to 1000 recent actions are stored in memory.
-
interactive.imagetool: remember last used loader for each tool (eb0cd2f)
- interactive.imagetool: fix code generation behaviour for non-uniform coordinates (3652a21)
- interactive.imagetool: preparation for saving and loading state (eca8262)
- erlab.io: regression in handling getattr of dataloader (dd0a568)
-
interactive.imagetool: Integrate data loaders to imagetool (7e7ea25)
A new property called
file_dialog_methods
can be set in each loader which determines the method and name that is used in the file chooser window in imagetool. -
accessors.kspace:
hv_to_kz
now accepts iterables (36770d7)
-
analysis.gold: add function for quick resolution fitting (2fae1c3)
-
analysis.fit: Add background option to
MultiPeakModel
andMultiPeakFunction
(2ccd8ad)
- erlab.io.plugins: fix for hv-dependent data (d52152f)
- erlab.io.plugins: support SSRL hv dependent data (1529b6a)
- cleanup namespace (847fbbe)
- interactive.imagetool: fix regression with nonuniform data (67df972)
- re-trigger due to CI failure (b6d69b5)
-
interactive.imagetool: add bin amount label to binning controls (7a7a692)
-
add accessor for selecting around a point (aa24457)
-
accessors.fit: add support for background models (550be2d)
If one coordinate is given but there are two independent variables are present in the model, the second one will be treated as the data. This makes the accessor compatible with y-dependent background models, such as the Shirley background provided in
lmfitxps
. -
io: make the dataloader behavior more customizable (4824127)
Now, a new
average_attrs
class attribute exists for attributes that would be averaged over multiple file scans. The current default just takes the attributes from the first file. This also works when you wish to demote a coordinate to an attribute while averaging over its values.For more fine-grained control of the resulting data attributes, a new method
combine_attrs
can be overridden to take care of attributes for scans over multiple files. The default behavior is to just use the attributes from the first file.
- plotting: make
gradient_fill
keep axis scaling (51507dd)
-
analysis.image: add check for 2D and uniform inputs (22bb02d)
-
try to fix synced itool garbage collection (932cc5a)
This only happens in GH actions, and it doesn't happen every time so it's hard to debug.
-
create utils subpackage to host internal methods (3fa2873)
The parallel module is now part of utils, without a compatibiliity layer or deprecation warning since nobody is using the functions from parallel anyway.
-
add deprecation warnings for utilities (5d375b8)
All submodules named
utilities.py
have been renamed toutils.py
for consistency. The old call toutilities.py
will still work but will raise a warning. The modules will be removed on 3.0 release. -
rename
erlab.interactive.utilities
toerlab.interactive.utils
(d9f1fb0) -
rename
erlab.analysis.utilities
toerlab.analysis.utils
(ed81b62) -
rename
erlab.io.utilities
toerlab.io.utils
(6e0813d) -
io.plugins.merlin: regard temperature as coordinate (2fda047)
- io.plugins.maestro: load correct beta for non deflector scans (5324c36)
-
io.utilities:
get_files
now only list files, not directories (60f9230) -
accessors.fit: add
make_params
call before determining param names, closes #38 (f1d161d) -
analysis.fit: make some models more robust to DataArray input (afe5ddd)
-
add loader for ALS BL7 MAESTRO
.h5
files (4f33402) -
interactive: add informative error message for missing Qt bindings (560615b)
-
io: rename some internal variables and reorder (76fe284)
Also added a check for astropy in FITS file related utility.
-
make mathtext copy default to svg (2f6e0e5)
-
resolve MemoryError in prominent color estimation (3bdcd03)
Due to numpy/numpy/#11879 changed the auto method to sqrt. This should also improve memory usage and speed, with little to no impact on the end result.
-
Gradient fill disappears upon adding labels
-
fit.models: wrong StepEdgeModel guess with DataArray input (6778c8d)
- plotting: code cleanup (aef10e4)
-
extended interactive accessor (f6f19ab)
The
qshow
accessor has been updated so that it callshvplot
(if installed) for data not supported by ImageTool.Also, the
qshow
accessor has been introduced to Datasets. For valid fit result datasets produced by themodelfit
accessor, callingqshow
will now show anhvplot
-based interactive visualization of the fit result. -
itool: make itool accept Datasets (f77b699)
When a Dataset is passed to
itool
, each data variable will be shown in a separate ImageTool window. -
analysis.image: add multidimensional Savitzky-Golay filter (131b32d)
-
itool: add input data dimension check (984f2db)
-
analysis.image: correct argument order parsing in some filters (6043413)
-
interactive: improve formatting for code copied to clipboard (d8b6d91)
- plotting: update
clean_labels
to useAxes.label_outer
(0c64756)
-
ktool: resolve ktool initialization problem, closes #32 (e88a58e)
-
itool: disable flag checking for non-numpy arrays (da6eb1d)
-
plotting: fix wrong regex in
scale_units
(d7826d0) -
fix bug in
modelfit
parameter concatenation (edaa556) -
itool: ensure DataArray is readable on load (5a0ff00)
-
imagetool: add method to update only the values (ca40fe4)
-
add interpolation along a path (7366ec4)
The
slice_along_path
function has been added toanalysis.interpolate
, which enables easy interpolation along a evenly spaced path that is specified by its vertices and step size. The path can have an arbitrary number of dimensions and points.
-
io: remove direct display call in interactive summary (d44b3a5)
This was causing duplicated plots.
-
plotting: add some validation checks to
plot_array
(2e0753c)The functions
plot_array
andplot_array_2d
now checks if the input array coordinates are uniformly spaced. If they are not, a warning is issued and the user is informed that the plot may not be accurate. -
plotting: increase default colorbar size (3208399)
The default
width
argument tonice_colorbar
is changed to 8 points. This ensures visibility in subplots, especially when constrained layout is used. -
delay interactive imports until called (ad15910)
-
various cleanup (2b38397)
Improve docstring formatting and tweak linter settings
-
io: make summary caching togglable (99b8e22)
Also fixes a bug where interactive summary plots were duplicated
-
io: data loader related fixes (da08e90)
DA30 dataloader now preserves case for attribute names from zip files.
Post processing for datasets now works properly
- interactive: keep pointer for imagetool, fix typing issues (c98c38e)
- move
characterization
toio
(9c30f1b)
-
kspace: rewrite conversion with
xarray.apply_ufunc
(156cef8)Momentum conversion now relies on xarray broadcasting for all computations, and objects with extra dimensions such as temperature can be automatically broadcasted.
Dask arrays can also be converted.
-
exampledata: enable specifying seed for noise rng (aa542e8)
-
interpolate: enable fast interpolation for 1D arrays (ff333a0)
-
make both arguments optional for loader_context (6780197)
-
kspace: automatically detect kinetic energy axis and convert to binding (bbde447)
-
add more output and parallelization to fit accessor (59b35f5)
Allows dictionary of
DataArray
s as parameter to fit accessor.Now, the return
Dataset
contains the data and the best fit array. Relevant tests have been added. -
add callable fit accessor using apply_ufunc (11e3546)
Add a
Dataset.modelfit
andDataArray.modelfit
accessor with similar syntax and output asDataset.curvefit
. Closes #22 -
add option to plot_array_2d so that users can pass non-normalized color array (74cf961)
-
analysis.gold: add option to normalize energy axis in fitting (3dffad6)
This improves performance and results when eV is large like ~100eV.
-
kspace: allow explicit coordinate kwargs (fe47efc)
-
exampledata: change noise generation parameters (b213f11)
-
fit: make FermiEdge2dModel compatible with flattened meshgrid-like input arrays (c0dba26)
-
fix progress bar for parallel objects that return generators (23d41b3)
Tqdm imports are also simplified. We no longer handle
is_notebook
ourselves, but just import fromtqdm.auto
-
plotting: fix 2d colormaps (8299576)
Allow images including nan to be plotted with gen_2d_colormap, also handle plot_array_2d colorbar aspect
-
make zip strict (ruff B905) (78bf5f5)
-
fix some type hints (2dfa5e1)
-
example: move exampledata from interactive to io (1fc7e6c)
Also add sample data generation for fermi edge
-
refactor accessors as submodule (9fc37bd)
-
rewrite either_dict_or_kwargs with public api (34953d1)
-
move correct_with_edge from era.utilities to era.gold (08a906f)
Calling from utilities will now raise a DeprecationWarning.
The erlab.analysis namespace is unchanged, so the affect will be minimal.
-
qsel now raises a warning upon scalar indexing outside coordinate bounds (d6ed628)
-
io: unify call signature for summarize (e2782c8)
-
resolve failing tests due to changes in sample data generation (80f0045)
-
interactive.exampledata: properly generate 2D data (825260c)
- io: speedup merlin summary generation by excluding duplicates (d6b4253)
-
io: allow for more complex setups (f67b2e4)
LoaderBase.infer_index now returns a second argument, which is a dictionary containing optional keyword arguments to load.
-
io: provide rich interactive summary (b075a9e)
-
io: include "Path" column in ssrl loader summary (ae1d8ae)
-
io: improve array formatting in summary (1718529)
-
fit: add sigma and amplitude expressions to MultiPeakModel parameters (3f6ba5e)
-
fit.minuit: properly handle parameters constrained with expressions (d03f012)
-
set informative model name for MultiPeakModel (d14ee9d)
-
add gaussian and lorentzian for consistency (07c0dfb)
-
enable component evaluation for MultiPeakModel (8875b74)
-
analysis.fit: add BCS gap equation and Dynes formula (f862aa4)
- curvefittingtool errors (9abb99c)
-
cleanup fit namespace (906aa99)
-
rename ExtendedAffineBroadenedFD to FermiEdgeModel (a98aa82)
-
interactive: exclude bad colormaps (877c915)
- interactive: update data load functions used in imagetool (c3abe35)
-
io: prevent specifying invalid data_dir (701b011)
-
io: fixes merlin summary data type resolving (a91ad3d)
-
io: fix summary loading (a5dd84a)
-
io: enable specifying data_dir in loader context manager (37913b8)
-
io: allow loader_class aliases to be None (7eae2eb)
-
interactive: overhaul dtool (8e5ec38)
Now supports interpolation, copying code, opening in imagetool, and 2D laplacian method.
-
interactive: improve code generation (7cbe857)
Automatically shortens code and allows literals in kwargs
-
interactive: extend xImageItem, add right-click menu to open imagetool (2b5bb2d)
-
sign error in minimum gradient (c45be0c)
-
analysis.image: normalize data for mingrad output for numerical stability (0fc3711)
- io: validation now defaults to warning instead of raising an error (8867a07)
-
PolyFunc
is nowPolynomialFunction
, andFermiEdge2dFunc
is nowFermiEdge2dFunction
. The corresponding model names are unchanged. (20d784c) -
This change disables the use of guess_fit. All fitting must be performed in the syntax recommended by lmfit. Addition of a accessor or a convenience function for coordinate-aware fitting is planned in the next release. (59163d5)
-
itool: add copy code to PlotItem vb menu (7b4f30a)
For each plot in imagetool, a new 'copy selection code' button has been added to the right-click menu that copies the code that can slice the data to recreate the data shown in the plot.
-
plotting: add N argument to plot_array_2d (2cd79f7)
-
add scaled laplace (079e1d2)
-
add gaussian filter and laplacian (8628d33)
-
add derivative module with minimum gradient implementation (e0eabde)
-
fit: directly base models on lmfit.Model (59163d5)
-
dynamic: properly broadcast xarray input (2f6672f)
-
fit.functions: polynomial function now works for xarray input (3eb80de)
-
analysis.image: remove critical typo (fb7de0f)
-
analysis.image: dtype safety of cfunc (b4f9b17)
-
set autodownsample off for colorbar (256bf2d)
-
disable itool downsample (e626bba)
-
itool: add explicit signatures to fastbinning (62e1d51)
Speedup initial binning by providing explicit signatures.
-
fit: unify dynamic function names (20d784c)
-
update dtool to use new functions (a6e46bb)
-
analysis.image: add documentation and reorder functions (340665d)
-
rename module to image and add citation (b74a654)
-
dtool: cleanup unused code (f4abd34)
- make imports work without optional pip dependencies (b8ac11d)
- load colormaps only when igor2 is available (7927c7d)
- leave out type annotation for passing tests (eb25008)
- igor2 does not have to be installed on import time (186727a)
- remove all pypi dependencies from pyproject.toml (1b2fd55)
- remove ktool_old (18ea072)
- add mdctool (a4976f9)
- remove deprecated function and dependencies (4b9c7b1)
-
set values after setting bounds (ab6d682)
-
proper patch all interpolator selection functions (b91834e)
-
make bz voronoi robust (8259760)
-
remove debug print statement in FastInterpolator class (712bd2c)
-
add edge correction (87adcef)
-
change variable name (b68949e)
-
make rotation transformations try fast interpolator first (e0a7908)
-
update warning message (af67c1a)
-
add several new accessors (664e92a)
-
use new accessors and attrs (8e1dee2)
-
add qplot accessor (cb9aa01)
-
remove annotate_cuts (004ee80)
-
dataloader cleanup (fd97780)
-
restore argname detection that was broken with namespace changes (863b702)
-
namespace collision (10edcdc)
-
followup namespace change (4c5222c)
-
allow offsetview upate chaining (8d5ca4f)
This also means that repr_html is automatically displayed when update or reset is called.
-
improve consistency in accessors (9596fd7)
Added setter method for configuration too.
-
make prints consistent (0021302)
-
change module names to prevent conflict with function names (493a5aa)
Cleanup erplot namespace and move tools to interactive.
-
follow class naming conventions (efb9610)
- add interactive tool to kspace accessor (fb91cdb)
- accessors are now registered upon package import (d79fee2)
-
update package metadata (ecfb88f)
This should be classified as chore, but commiting as a fix to trigger CI
-
calculate kz in MomentumAccessor (46979f9)
Add method that calculates kz array from given photon energy float
-
make momentum conversion functions xarray compatible (a7aa34b)
- io: add new data loader plugin for DA30 + SES (7a27a2f)
-
io: properly handle registry getattr (499526f)
This fixes an issue where repr_html will fallback to repr.
Additionally,
get
will now raise a KeyError instead of a ValueError.