Miscellaneous improvements #69

kmnhan · 2024-11-19T05:10:32Z

This should be the last PR prior to 3.1.0 release.

If numba 0.61 arrives soon, explicit python 3.13 support will also be incorporated here.

codecov · 2024-11-19T05:21:01Z

❌ 2 Tests Failed:

Tests completed	Failed	Passed	Skipped
735	2	733	0

View the top 2 failed tests by shortest run time

tests.interactive.test_imagetool::test_itool_rotate

Stack Traces | 0.525s run time

qtbot = <pytestqt.qtbot.QtBot object at 0x7fd26d6f86e0>
accept_dialog = <class 'tests.conftest._DialogHandler'>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m #x1B[92mtest_itool_rotate#x1B[39;49;00m(qtbot, accept_dialog):#x1B[90m#x1B[39;49;00m
        data = xr.DataArray(np.arange(#x1B[94m25#x1B[39;49;00m).reshape((#x1B[94m5#x1B[39;49;00m, #x1B[94m5#x1B[39;49;00m)).astype(#x1B[96mfloat#x1B[39;49;00m), dims=[#x1B[33m"#x1B[39;49;00m#x1B[33mx#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33my#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
        win = itool(data, execute=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        qtbot.addWidget(win)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# Test dialog#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mdef#x1B[39;49;00m #x1B[92m_set_dialog_params#x1B[39;49;00m(dialog: RotationDialog) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            dialog.angle_spin.setValue(#x1B[94m60.0#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            dialog.reshape_check.setChecked(#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            dialog.new_window_check.setChecked(#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        accept_dialog(win.mnb._rotate, pre_call=_set_dialog_params)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# Check if the data is rotated#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        xarray.testing.assert_allclose(#x1B[90m#x1B[39;49;00m
            win.slicer_area._data,#x1B[90m#x1B[39;49;00m
            erlab.analysis.transform.rotate(data, angle=#x1B[94m60.0#x1B[39;49;00m, reshape=#x1B[94mTrue#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# Test guidelines#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        win.slicer_area.set_data(data)#x1B[90m#x1B[39;49;00m
        win.slicer_area.main_image.set_guidelines(#x1B[94m3#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m win.slicer_area.main_image.is_guidelines_visible#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        win.slicer_area.main_image._guidelines_items[#x1B[94m0#x1B[39;49;00m].setAngle(#x1B[94m90.0#x1B[39;49;00m - #x1B[94m30.0#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        win.slicer_area.main_image._guidelines_items[-#x1B[94m1#x1B[39;49;00m].setPos((#x1B[94m3.0#x1B[39;49;00m, #x1B[94m3.1#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mdef#x1B[39;49;00m #x1B[92m_set_dialog_params#x1B[39;49;00m(dialog: RotationDialog) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94massert#x1B[39;49;00m dialog.angle_spin.value() == #x1B[94m30.0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94massert#x1B[39;49;00m dialog.center_spins[#x1B[94m0#x1B[39;49;00m].value() == #x1B[94m3.0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94massert#x1B[39;49;00m dialog.center_spins[#x1B[94m1#x1B[39;49;00m].value() == #x1B[94m3.1#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            dialog.copy_button.click()#x1B[90m#x1B[39;49;00m
            dialog.reshape_check.setChecked(#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            dialog.new_window_check.setChecked(#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        accept_dialog(win.mnb._rotate, pre_call=_set_dialog_params)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# Check if the data is rotated#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        xarray.testing.assert_allclose(#x1B[90m#x1B[39;49;00m
            win.slicer_area._data,#x1B[90m#x1B[39;49;00m
            erlab.analysis.transform.rotate(#x1B[90m#x1B[39;49;00m
                data, angle=#x1B[94m30.0#x1B[39;49;00m, center=(#x1B[94m3.0#x1B[39;49;00m, #x1B[94m3.1#x1B[39;49;00m), reshape=#x1B[94mTrue#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            ),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# Test copy button#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m pyperclip.paste().startswith(#x1B[33m"#x1B[39;49;00m#x1B[33mera.transform.rotate#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# Transpose should remove guidelines#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        qtbot.keyClick(win, QtCore.Qt.Key.Key_T)#x1B[90m#x1B[39;49;00m
>       #x1B[94massert#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m win.slicer_area.main_image.is_guidelines_visible#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       assert not True#x1B[0m
#x1B[1m#x1B[31mE        +  where True = <erlab.interactive.imagetool.core.ItoolPlotItem object at 0x7fd2385cd4f0>.is_guidelines_visible#x1B[0m
#x1B[1m#x1B[31mE        +    where <erlab.interactive.imagetool.core.ItoolPlotItem object at 0x7fd2385cd4f0> = <erlab.interactive.imagetool.core.ImageSlicerArea object at 0x7fd23889de50>.main_image#x1B[0m
#x1B[1m#x1B[31mE        +      where <erlab.interactive.imagetool.core.ImageSlicerArea object at 0x7fd23889de50> = <erlab.interactive.imagetool.ImageTool object at 0x7fd23889def0>.slicer_area#x1B[0m

#x1B[1m#x1B[31mtests/interactive/test_imagetool.py#x1B[0m:426: AssertionError

tests.interactive.test_imagetool::test_itool_load

Stack Traces | 0.881s run time

qtbot = <pytestqt.qtbot.QtBot object at 0x7fd24012ecf0>
move_and_compare_values = <function _move_and_compare_values at 0x7fd26fae9800>
accept_dialog = <class 'tests.conftest._DialogHandler'>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m #x1B[92mtest_itool_load#x1B[39;49;00m(qtbot, move_and_compare_values, accept_dialog):#x1B[90m#x1B[39;49;00m
        data = xr.DataArray(#x1B[90m#x1B[39;49;00m
            np.arange(#x1B[94m25#x1B[39;49;00m).reshape((#x1B[94m5#x1B[39;49;00m, #x1B[94m5#x1B[39;49;00m)),#x1B[90m#x1B[39;49;00m
            dims=[#x1B[33m"#x1B[39;49;00m#x1B[33mx#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33my#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
            coords={#x1B[33m"#x1B[39;49;00m#x1B[33mx#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: np.arange(#x1B[94m5#x1B[39;49;00m), #x1B[33m"#x1B[39;49;00m#x1B[33my#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m: np.arange(#x1B[94m5#x1B[39;49;00m)},#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        win = itool(np.zeros((#x1B[94m2#x1B[39;49;00m, #x1B[94m2#x1B[39;49;00m)), execute=#x1B[94mFalse#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        qtbot.addWidget(win)#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m qtbot.waitExposed(win):#x1B[90m#x1B[39;49;00m
            win.show()#x1B[90m#x1B[39;49;00m
            win.activateWindow()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        tmp_dir = tempfile.TemporaryDirectory()#x1B[90m#x1B[39;49;00m
        filename = #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mtmp_dir.name#x1B[33m}#x1B[39;49;00m#x1B[33m/data.h5#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        data.to_netcdf(filename, engine=#x1B[33m"#x1B[39;49;00m#x1B[33mh5netcdf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mdef#x1B[39;49;00m #x1B[92m_go_to_file#x1B[39;49;00m(dialog: QtWidgets.QFileDialog):#x1B[90m#x1B[39;49;00m
            dialog.setDirectory(tmp_dir.name)#x1B[90m#x1B[39;49;00m
            dialog.selectFile(filename)#x1B[90m#x1B[39;49;00m
            focused = dialog.focusWidget()#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[96misinstance#x1B[39;49;00m(focused, QtWidgets.QLineEdit):#x1B[90m#x1B[39;49;00m
                focused.setText(#x1B[33m"#x1B[39;49;00m#x1B[33mdata.h5#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        accept_dialog(#x1B[94mlambda#x1B[39;49;00m: win._open_file(native=#x1B[94mFalse#x1B[39;49;00m), pre_call=_go_to_file)#x1B[90m#x1B[39;49;00m
>       move_and_compare_values(qtbot, win, [#x1B[94m12.0#x1B[39;49;00m, #x1B[94m7.0#x1B[39;49;00m, #x1B[94m6.0#x1B[39;49;00m, #x1B[94m11.0#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/interactive/test_imagetool.py#x1B[0m:73: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31mtests/conftest.py#x1B[0m:272: in _move_and_compare_values
    #x1B[0massert_almost_equal(win.array_slicer.point_value(cursor), expected[#x1B[94m1#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

args = (np.float64(12.0), 7.0), kwds = {}

    #x1B[0m#x1B[37m@wraps#x1B[39;49;00m(func)#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m #x1B[92minner#x1B[39;49;00m(*args, **kwds):#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._recreate_cm():#x1B[90m#x1B[39;49;00m
>           #x1B[94mreturn#x1B[39;49;00m func(*args, **kwds)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           AssertionError: #x1B[0m
#x1B[1m#x1B[31mE           Arrays are not almost equal to 7 decimals#x1B[0m
#x1B[1m#x1B[31mE            ACTUAL: np.float64(12.0)#x1B[0m
#x1B[1m#x1B[31mE            DESIRED: 7.0#x1B[0m

#x1B[1m#x1B[.../hostedtoolcache/Python/3.12.7.../x64/lib/python3.12/contextlib.py#x1B[0m:81: AssertionError

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…rlab.constants`

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`, and `colorcet`. The user must add manual import statements.

…cache tools

…conActionButton

… for 1D

…space Enables users to save multiple ImageTool windows to a single file using the manager.

…goldtool

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.

kmnhan added 4 commits November 19, 2024 13:41

docs: add docstring

307f84a

refactor(plotting): streamline igor CT loading

e1e8baa

docs(accessors.kspace): make decorators private

69ce4aa

chore: add emojis to changelog!

4285f0b

refactor: move AxesConfiguration from erlab.analysis.kspace to `e…

3593d41

…rlab.constants`

kmnhan force-pushed the dev-2411 branch from 4ecd38d to 34354c7 Compare November 19, 2024 06:25

perf: 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`, and `colorcet`. The user must add manual import statements.

kmnhan force-pushed the dev-2411 branch from 34354c7 to d7f3b3c Compare November 19, 2024 06:27

kmnhan added 3 commits November 19, 2024 20:17

fix(io.dataloader): allow dimensions without coordinates in output data

752facf

feat(io.plugins): add summary generation to maestro loader

aa6f5d2

perf(io): implement lazy loading for h5netcdf and nexusformat imports

3f219ae

kmnhan force-pushed the dev-2411 branch from 503bd65 to 3f219ae Compare November 19, 2024 12:25

kmnhan added 15 commits November 20, 2024 16:38

chore: cleanup

e939419

fix(io.plugins.maestro): fix wrong temperature attribute

6ed2a70

chore: use pathlib

6b4e77c

chore: move internal function to utils

b724033

refactor(interactive.imagetool): use HDF5 files instead of pickle to …

be66297

…cache tools

chore: cleanup deprecated code

f1cc59e

fix(interactive.imagetool): cursor sync for non-uniform coords

4aa1425

refactor(interactive): move IconButton to interactive utils and add I…

e78190f

…conActionButton

feat(interactive.imagetool.manager): add menubar to manager

59326a1

refactor(io.dataloader): improve warning messages and error handling

1ebfa72

feat(interactive.imagetool): change manager icon

3e20e63

chore: move some menubar methods to ImageTool

c9a5496

feat(interactive.imagetool): show dialog when data is being loaded

5577249

refactor(plotting.general): use matplotlib api instead of xarray plot…

9e38b2c

… for 1D

fix(io.plugins.merlin): fix match signature

5586cce

kmnhan force-pushed the dev-2411 branch from 1a06c3c to 5586cce Compare November 22, 2024 05:07

feat(interactive.imagetool): add save and load functionality for work…

a5d38af

…space Enables users to save multiple ImageTool windows to a single file using the manager.

kmnhan added 9 commits November 22, 2024 15:28

ci(pre-commit): update pre-commit hooks

c1cf7c7

style: combine interactive tool classes

ac5ac92

test: catch warnings

cb733d1

fix(interactive.imagetool): retain axis order when opening dtool and …

e14c9fc

…goldtool

fix(interactive.imagetool): resolve segfault on save current data

5699fa3

fix(io.plugins.lorea): fix file dialog method

4c74105

test: refactor imagetool tests

6352047

feat(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.

style: update type hints to support xarray 2024.11.0

c464a3a

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Miscellaneous improvements #69

Miscellaneous improvements #69

kmnhan commented Nov 19, 2024 •

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Miscellaneous improvements #69

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Miscellaneous improvements #69

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❌ 2 Tests Failed:

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