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@@ -58,3 +58,25 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_A.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_A_none.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_A_overlap.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_A_patch.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_B.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_B_unadjusted.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_C.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_C_nophase.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_kernelsynth_both.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_kernelsynth_none.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_kernelsynth_patch.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_kernelsynth_stride.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_pure_both.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_pure_none.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_pure_patch.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_pure_stride.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_tsmixup_both.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_tsmixup_none.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_tsmixup_patch.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D1_tsmixup_stride.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D2_stride.nc filter=lfs diff=lfs merge=lfs -text
+clean_15model/04_D2_stride_deltahat.nc filter=lfs diff=lfs merge=lfs -text

bayes_no_s5s15s28.log

@@ -0,0 +1,10 @@
+  exists 02_collapse.parquet
+  exists 02_contrasts.parquet
+  exists 02_mdl_bandtasks.parquet
+  exists 02_mdl_cells.parquet
+  exists 02_sites.parquet
+
+Data ready in C:\Users\feder\Desktop\patchAliasing\chronos\bayesian\_run\full_no_s5s15s28\data
+Starting notebook execution (this will take several hours) ...
+
+cmd: C:\Users\feder\AppData\Local\Programs\Python\Python312\python.exe -m nbconvert --to notebook --execute --ExecutePreprocessor.timeout -1 --output C:\Users\feder\Desktop\patchAliasing\chronos\bayesian\bayesian_analysis_executed.ipynb C:\Users\feder\Desktop\patchAliasing\chronos\bayesian\bayesian_analysis.ipynb

bayes_no_s5s15s28.log.err

@@ -0,0 +1,92 @@
+[NbConvertApp] Converting notebook C:\Users\feder\Desktop\patchAliasing\chronos\bayesian\bayesian_analysis.ipynb to notebook
+C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\zmq\_future.py:718: RuntimeWarning: Proactor event loop does not implement add_reader family of methods required for zmq. Registering an additional selector thread for add_reader support via tornado. Use `asyncio.set_event_loop_policy(WindowsSelectorEventLoopPolicy())` to avoid this warning.
+  self._get_loop()
+[IPKernelApp] WARNING | Kernel is running over TCP without encryption. All communication (including code and outputs) is sent in plain text and is susceptible to eavesdropping. Use IPC transport or launch with kernel manager-provisioned CurveZMQ keys to enable transport encryption.
+Traceback (most recent call last):
+  File "<frozen runpy>", line 198, in _run_module_as_main
+  File "<frozen runpy>", line 88, in _run_code
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\__main__.py", line 5, in <module>
+    main()
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\jupyter_core\application.py", line 284, in launch_instance
+    super().launch_instance(argv=argv, **kwargs)
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\traitlets\config\application.py", line 1080, in launch_instance
+    app.start()
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\nbconvertapp.py", line 420, in start
+    self.convert_notebooks()
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\nbconvertapp.py", line 597, in convert_notebooks
+    self.convert_single_notebook(notebook_filename)
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\nbconvertapp.py", line 563, in convert_single_notebook
+    output, resources = self.export_single_notebook(
+                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\nbconvertapp.py", line 487, in export_single_notebook
+    output, resources = self.exporter.from_filename(
+                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\exporters\exporter.py", line 201, in from_filename
+    return self.from_file(f, resources=resources, **kw)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\exporters\exporter.py", line 220, in from_file
+    return self.from_notebook_node(
+           ^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\exporters\notebook.py", line 36, in from_notebook_node
+    nb_copy, resources = super().from_notebook_node(nb, resources, **kw)
+                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\exporters\exporter.py", line 154, in from_notebook_node
+    nb_copy, resources = self._preprocess(nb_copy, resources)
+                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\exporters\exporter.py", line 353, in _preprocess
+    nbc, resc = preprocessor(nbc, resc)
+                ^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\preprocessors\base.py", line 48, in __call__
+    return self.preprocess(nb, resources)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\preprocessors\execute.py", line 103, in preprocess
+    self.preprocess_cell(cell, resources, index)
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbconvert\preprocessors\execute.py", line 124, in preprocess_cell
+    cell = self.execute_cell(cell, index, store_history=True)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\jupyter_core\utils\__init__.py", line 165, in wrapped
+    return loop.run_until_complete(inner)
+           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\asyncio\base_events.py", line 691, in run_until_complete
+    return future.result()
+           ^^^^^^^^^^^^^^^
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbclient\client.py", line 1062, in async_execute_cell
+    await self._check_raise_for_error(cell, cell_index, exec_reply)
+  File "C:\Users\feder\AppData\Local\Programs\Python\Python312\Lib\site-packages\nbclient\client.py", line 918, in _check_raise_for_error
+    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
+nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
+------------------
+# Run the collection. Already-complete geometries are skipped without loading their model, so this
+# cell is safe to re-run after a disconnect.
+if HAVE_TORCH:
+    DATA = collect.collect_all(DATA_DIR, models=pl.MODELS, cfg=CFG)
+else:
+    print("torch is not available in this runtime: loading the tables written by a previous "
+          "GPU run instead (this is the intended CPU-runtime path).")
+    DATA = {name: pd.read_parquet(DATA_DIR / f"02_{name}.parquet")
+            for name in collect.TABLES if (DATA_DIR / f"02_{name}.parquet").exists()}
+    collect.check_design(DATA)
+
+contrasts = DATA["contrasts"]
+mdl_cells = DATA["mdl_cells"]
+collapse = DATA["collapse"]
+sites = DATA["sites"]
+bandtasks = DATA.get("mdl_bandtasks")
+
+# Drop geometries with S in EXCLUDE_S before any model sees the data.
+for _tbl in ["contrasts", "mdl_cells", "collapse", "sites"]:
+    globals()[_tbl] = globals()[_tbl][~globals()[_tbl]["S"].isin(EXCLUDE_S)].reset_index(drop=True)
+if bandtasks is not None:
+    bandtasks = bandtasks[~bandtasks["S"].isin(EXCLUDE_S)].reset_index(drop=True)
+
+print("
+rows after EXCLUDE_S filter:", {k: len(globals()[k]) for k in ["contrasts", "mdl_cells", "collapse", "sites"]})
+------------------
+
+
+  Cell In[13], line 24
+    print("
+          ^
+SyntaxError: unterminated string literal (detected at line 24)
+
+

clean_15model/01_prior_spec.json

@@ -0,0 +1,18 @@
+{
+  "prior_scale": 0.5,
+  "prior_ladder": [
+    0.25,
+    0.5,
+    1.0
+  ],
+  "nu": 4,
+  "attenuation_20": -0.2231435513142097,
+  "rope_log": 0.09531017980432493,
+  "rope_slope": 0.1,
+  "p_attenuation20_prior": 0.33585,
+  "p_sigma_phase_in_rope_prior": 0.2987,
+  "p_kappaS_in_rope_prior": 0.0479,
+  "planned_contrast_rows": 22260,
+  "smoke": false,
+  "seed": 42
+}

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clean_15model/03_recovery.parquet

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