Adding gates to a workspace and exporting as wsp

[ayilmaz52]

Hello, I have difficulties exporting a session as wsp. What I am currently doing:

1. Getting the Gating-strategy from a pre-saved workspace (wsp-file)
2. Creating a session with the sample and Gating-strategy
3. Creating a RectangleGate
4. Adding the Gate to the session
5. Exporting the session with session.export_wsp()

wsp = fk.Workspace(wsp_datei, fcs_files)
wsp.analyze_samples(sample_group, verbose=True)
gating_strategy = wsp.get_gating_strategy(sample_id)
session = fk.Session(gating_strategy=gating_strategy, fcs_samples=sample_path)
dim_a = fk.Dimension('PE-A', range_max=500, compensation_ref='FCS', transformation_ref='PE-A')
dim_b = fk.Dimension('BB700-A', range_min=1000, compensation_ref='FCS', transformation_ref='BB700-A')
rect_gate = fk.gates.RectangleGate('top-left', dimensions=[dim_a, dim_b])
session.analyze_samples(sample_id, verbose=True)
print(session.get_gate_hierarchy())
session.export_wsp(wsp_datei, 'All Samples')

That's the traceback I get:

Traceback (most recent call last):
File "C:\Users\Abdulkadir.Yilmaz\AppData\Roaming\JetBrains\PyCharmCE2021.2\scratches\scratch.py", line 121, in
session.export_wsp(wsp_datei, 'All Samples')
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_models\session.py", line 264, in export_wsp
wsp_utils.export_flowjo_wsp(self.gating_strategy, group_name, samples, file_handle)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 1077, in export_flowjo_wsp
_add_transform_to_wsp(xforms_el, dim, gating_strategy.get_transform(xform), ns_map)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 734, in _add_transform_to_wsp
raise NotImplementedError("Transform type %s is not yet supported" % type(transform))
NotImplementedError: Transform type <class 'flowkit._models.transforms._wsp_transforms.WSPBiexTransform'> is not yet supported

[whitews]

Hi, I can replicate this issue & will have a fix for it shortly.

[whitews]

Hi, this should be fixed in the latest develop branch. Let me know if it works for you.

[ayilmaz52]

Hello, thank you for the fast reply and implementation, but it still doesn't work. I am getting the following traceback:

Traceback (most recent call last):
File "C:\Users\Abdulkadir.Yilmaz\AppData\Roaming\JetBrains\PyCharmCE2021.2\scratches\scratch.py", line 121, in
session.export_wsp(wsp_datei, 'All Samples')
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_models\session.py", line 264, in export_wsp
wsp_utils.export_flowjo_wsp(self.gating_strategy, group_name, samples, file_handle)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 1092, in export_flowjo_wsp
_add_sample_node_to_wsp(
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 943, in _add_sample_node_to_wsp
_recurse_add_sub_populations(
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 904, in _recurse_add_sub_populations
_recurse_add_sub_populations(
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 904, in _recurse_add_sub_populations
_recurse_add_sub_populations(
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 904, in _recurse_add_sub_populations
_recurse_add_sub_populations(
[Previous line repeated 4 more times]
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 893, in _recurse_add_sub_populations
_add_rectangle_gate(gate_el, gate, fj_id, parent_fj_id, gating_strategy, comp_prefix, ns_map)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 827, in _add_rectangle_gate
dim_min = xform.inverse(np.array([[dim.min]]))[0, 0]
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_models\transforms_wsp_transforms.py", line 251, in inverse
new_events = self._inverse_lut_func(events)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\scipy\interpolate_polyint.py", line 79, in call
x, x_shape = self._prepare_x(x)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\scipy\interpolate_polyint.py", line 91, in _prepare_x
x = _asarray_validated(x, check_finite=False, as_inexact=True)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\scipy_lib_util.py", line 255, in _asarray_validated
raise ValueError('object arrays are not supported')
ValueError: object arrays are not supported

[whitews]

OK, looks like it got farther in the process. I pushed another fix for what I think is causing this. Can you try the latest develop branch again?

[ayilmaz52]

Sorry for the late answer, i had no time to further work on the project. It works now fine for RectangleGates.

With Quadrant gates there are still issues, I'm not sure if the problem is caused by my side, but I create the Quadrant gate as described in the tutorial.

gate_path = ('root', 'Time', 'Singlets', 'Cells', 'Viable', 'Lymphocytes', 'CD3+', 'CD3+CD8+')

quad_div1 = fk.QuadrantDivider('PE-A-div', 'PE-A', compensation_ref='FCS', values=[50000])
quad_div2 = fk.QuadrantDivider('BB700-A-div', 'BB700-A', compensation_ref='FCS', values=[50000])

quad_divs = [quad_div1, quad_div2]

quad_1 = fk.gates.Quadrant( quadrant_id='PEpos-BB700pos', divider_refs=['PE-A-div', 'BB700-A-div'], 
                            divider_ranges=[(500, None), (500, None)])
quad_2 = fk.gates.Quadrant(quadrant_id='PEpos-BB700neg', divider_refs=['PE-A-div', 'BB700-A-div'], 
                           divider_ranges=[(500, None), (None, 500)])
quad_3 = fk.gates.Quadrant(quadrant_id='PEneg-BB700pos', divider_refs=['PE-A-div', 'BB700-A-div'],
                           divider_ranges=[(None, 500), (500, None)])
quad_4 = fk.gates.Quadrant(quadrant_id='PEneg-BB700neg', divider_refs=['PE-A-div', 'BB700-A-div'], 
                           divider_ranges=[(None, 500), (None, 500)])

quadrants = [quad_1, quad_2, quad_3, quad_4]

quad_gate1 = fk.gates.QuadrantGate('Quadrant0', dividers=quad_divs, quadrants=quadrants)

session.add_gate(quad_gate1, gate_path=gate_path, sample_id=sample_id)

I want to create Quadrantgates as shown in the picture. The rectangle gates CD8+IFNg+, CD8+IL-2+, CD8+IL-2+ are already available. I want to add to the CD3+CD8+ path two Quadrantgates as shown in the picture, but i get a QuadrantReferenceError. It seems that the package can not handle the gate type.

The error-message:
Traceback (most recent call last):
File "C:\Users\Abdulkadir.Yilmaz\AppData\Roaming\JetBrains\PyCharmCE2021.2\scratches\scratch.py", line 122, in
session.export_wsp(wsp_datei, 'All Samples')
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_models\session.py", line 263, in export_wsp
wsp_utils.export_flowjo_wsp(self.gating_strategy, group_name, samples, file_handle)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_utils\wsp_utils.py", line 1036, in export_flowjo_wsp
gate = gating_strategy.get_gate(g_id, g_path)
File "C:\Users\Abdulkadir.Yilmaz\PycharmProjects\Flowkit_Test\venv\lib\site-packages\flowkit_models\gating_strategy.py", line 148, in get_gate
raise QuadrantReferenceError(
flowkit.exceptions.QuadrantReferenceError: PEpos-BB700pos references a Quadrant, specify the owning QuadrantGate GateNode('/root/Time/Singlets/Cells/Viable/Lymphocytes/CD3+/CD3+CD8+/CD3+CD8+', custom_gates={}, gate=QuadrantGate(CD3+CD8+, quadrants: 4), gate_type='QuadrantGate') instead