diff --git a/.buildinfo b/.buildinfo index 445de37..de33cb8 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: f7b8bbf314faca13609374c7e75f8901 +config: 626d65cb49cf40e93737d854be8e1c81 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_sources/autoapi/overlappogram/index.rst.txt b/_sources/autoapi/overlappogram/index.rst.txt index ccb7c70..857e30c 100644 --- a/_sources/autoapi/overlappogram/index.rst.txt +++ b/_sources/autoapi/overlappogram/index.rst.txt @@ -106,6 +106,12 @@ Package Contents + .. py:attribute:: _n_iter + :type: numpy.ndarray | None + :value: None + + + .. py:attribute:: _thread_count_lock diff --git a/_sources/autoapi/overlappogram/inversion/index.rst.txt b/_sources/autoapi/overlappogram/inversion/index.rst.txt index b43523d..32e2e6c 100644 --- a/_sources/autoapi/overlappogram/inversion/index.rst.txt +++ b/_sources/autoapi/overlappogram/inversion/index.rst.txt @@ -83,6 +83,12 @@ Module Contents + .. py:attribute:: _n_iter + :type: numpy.ndarray | None + :value: None + + + .. py:attribute:: _thread_count_lock diff --git a/_static/documentation_options.js b/_static/documentation_options.js index ed7cf3c..c04a1db 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.0.9', + VERSION: '0.0.10', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/autoapi/index.html b/autoapi/index.html index 1f96baa..8e6ecfe 100644 --- a/autoapi/index.html +++ b/autoapi/index.html @@ -8,7 +8,7 @@ -
overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/autoapi/overlappogram/cli/index.html b/autoapi/overlappogram/cli/index.html index 6717038..d5982f5 100644 --- a/autoapi/overlappogram/cli/index.html +++ b/autoapi/overlappogram/cli/index.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/autoapi/overlappogram/error/index.html b/autoapi/overlappogram/error/index.html index 40812fb..43f3d4a 100644 --- a/autoapi/overlappogram/error/index.html +++ b/autoapi/overlappogram/error/index.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/autoapi/overlappogram/index.html b/autoapi/overlappogram/index.html index e412732..d980b8e 100644 --- a/autoapi/overlappogram/index.html +++ b/autoapi/overlappogram/index.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
@@ -552,6 +552,11 @@Inverter._row_scores
Inverter._overlappogram_width
Inverter._overlappogram_height
Inverter._n_iter
Inverter._thread_count_lock
Inverter._response_meta
Inverter._progress_bar
overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
@@ -528,6 +528,11 @@Inverter._row_scores
Inverter._overlappogram_width
Inverter._overlappogram_height
Inverter._n_iter
Inverter._thread_count_lock
Inverter._response_meta
Inverter._progress_bar
overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/autoapi/overlappogram/response/index.html b/autoapi/overlappogram/response/index.html index b226717..90edb3d 100644 --- a/autoapi/overlappogram/response/index.html +++ b/autoapi/overlappogram/response/index.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/autoapi/overlappogram/spectral/index.html b/autoapi/overlappogram/spectral/index.html index be27a26..d1e299f 100644 --- a/autoapi/overlappogram/spectral/index.html +++ b/autoapi/overlappogram/spectral/index.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/configuration.html b/configuration.html index eb1a651..c9e272c 100644 --- a/configuration.html +++ b/configuration.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/development.html b/development.html index bec9f87..03737c1 100644 --- a/development.html +++ b/development.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/examples.html b/examples.html index a649f0c..e1595a5 100644 --- a/examples.html +++ b/examples.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/genindex.html b/genindex.html index 8889e94..184662a 100644 --- a/genindex.html +++ b/genindex.html @@ -7,7 +7,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
@@ -460,6 +460,12 @@overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/index.html b/index.html index 51add43..64adb98 100644 --- a/index.html +++ b/index.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/objects.inv b/objects.inv index 45dba58..aa41ab8 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/overview.html b/overview.html index d6782b9..dc1cf64 100644 --- a/overview.html +++ b/overview.html @@ -8,7 +8,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/py-modindex.html b/py-modindex.html index acc31bb..a41e454 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -7,7 +7,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/search.html b/search.html index ed6aa71..9f20a73 100644 --- a/search.html +++ b/search.html @@ -6,7 +6,7 @@ -overlappogram 0.0.9 documentation
+overlappogram 0.0.10 documentation
diff --git a/searchindex.js b/searchindex.js index 6427fca..580ee2c 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API Reference": [[0, null]], "Attributes": [[1, "attributes"]], "Building the docs": [[9, "building-the-docs"]], "Chunked mode": [[13, "chunked-mode"]], "Classes": [[3, "classes"], [4, "classes"]], "Configuration": [[8, null]], "Contents:": [[12, null]], "Development": [[9, null]], "Examples": [[10, null]], "Exceptions": [[2, "exceptions"]], "Functions": [[1, "functions"], [3, "functions"], [5, "functions"], [6, "functions"], [7, "functions"]], "Help": [[11, null]], "Hybrid mode": [[13, "hybrid-mode"]], "Indices and tables": [[12, "indices-and-tables"]], "Installation": [[13, "installation"]], "Module Contents": [[1, "module-contents"], [2, "module-contents"], [4, "module-contents"], [5, "module-contents"], [6, "module-contents"], [7, "module-contents"]], "Optimization modes": [[13, "optimization-modes"]], "Overview": [[13, null]], "Package Contents": [[3, "package-contents"]], "Row mode": [[13, "row-mode"]], "Running": [[13, "running"]], "Running tests": [[9, "running-tests"]], "Setting up pre-commit": [[9, "setting-up-pre-commit"]], "Submodules": [[3, "submodules"]], "Welcome to overlappogram\u2019s documentation!": [[12, null]], "execution section": [[8, "execution-section"]], "inversion section": [[8, "inversion-section"]], "model section": [[8, "model-section"]], "output section": [[8, "output-section"]], "overlappogram": [[3, null]], "overlappogram.cli": [[1, null]], "overlappogram.error": [[2, null]], "overlappogram.inversion": [[4, null]], "overlappogram.io": [[5, null]], "overlappogram.response": [[6, null]], "overlappogram.spectral": [[7, null]], "paths section": [[8, "paths-section"]]}, "docnames": ["autoapi/index", "autoapi/overlappogram/cli/index", "autoapi/overlappogram/error/index", "autoapi/overlappogram/index", "autoapi/overlappogram/inversion/index", "autoapi/overlappogram/io/index", "autoapi/overlappogram/response/index", "autoapi/overlappogram/spectral/index", "configuration", "development", "examples", "help", "index", "overview"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["autoapi/index.rst", "autoapi/overlappogram/cli/index.rst", "autoapi/overlappogram/error/index.rst", "autoapi/overlappogram/index.rst", "autoapi/overlappogram/inversion/index.rst", "autoapi/overlappogram/io/index.rst", "autoapi/overlappogram/response/index.rst", "autoapi/overlappogram/spectral/index.rst", "configuration.rst", "development.rst", "examples.rst", "help.rst", "index.rst", "overview.rst"], "indexentries": {"_collect_results() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._collect_results", false]], "_collect_results() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._collect_results", false]], "_completed_row_count (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._completed_row_count", false]], "_completed_row_count (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._completed_row_count", false]], "_detector_row_range (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._detector_row_range", false]], "_detector_row_range (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._detector_row_range", false]], "_em_data (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._em_data", false]], "_em_data (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._em_data", false]], "_field_angle_range (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._field_angle_range", false]], "_field_angle_range (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._field_angle_range", false]], "_initialize_with_overlappogram() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._initialize_with_overlappogram", false]], "_initialize_with_overlappogram() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._initialize_with_overlappogram", false]], "_inversion_prediction (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._inversion_prediction", false]], "_inversion_prediction (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._inversion_prediction", false]], "_invert_image_row() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._invert_image_row", false]], "_invert_image_row() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._invert_image_row", false]], "_mode (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._mode", false]], "_mode (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._mode", false]], "_models (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._models", false]], "_models (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._models", false]], "_overlappogram (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._overlappogram", false]], "_overlappogram (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._overlappogram", false]], "_overlappogram_height (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._overlappogram_height", false]], "_overlappogram_height (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._overlappogram_height", false]], "_overlappogram_width (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._overlappogram_width", false]], "_overlappogram_width (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._overlappogram_width", false]], "_progress_bar (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._progress_bar", false]], "_progress_bar (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._progress_bar", false]], "_progress_indicator() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._progress_indicator", false]], "_progress_indicator() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._progress_indicator", false]], "_response_meta (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._response_meta", false]], "_response_meta (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._response_meta", false]], "_row_scores (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._row_scores", false]], "_row_scores (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._row_scores", false]], "_smooth_over (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._smooth_over", false]], "_smooth_over (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._smooth_over", false]], "_solution_fov_width (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._solution_fov_width", false]], "_solution_fov_width (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._solution_fov_width", false]], "_start_chunk_inversion() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._start_chunk_inversion", false]], "_start_chunk_inversion() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._start_chunk_inversion", false]], "_start_row_inversion() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._start_row_inversion", false]], "_start_row_inversion() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._start_row_inversion", false]], "_switch_to_row_inversion() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._switch_to_row_inversion", false]], "_switch_to_row_inversion() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._switch_to_row_inversion", false]], "_thread_count_lock (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._thread_count_lock", false]], "_thread_count_lock (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._thread_count_lock", false]], "_unconverged_rows (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._unconverged_rows", false]], "_unconverged_rows (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._unconverged_rows", false]], "create_spectrally_pure_images() (in module overlappogram.spectral)": [[7, "overlappogram.spectral.create_spectrally_pure_images", false]], "invaliddataformaterror": [[2, "overlappogram.error.InvalidDataFormatError", false]], "invalidinversionmodeerror": [[2, "overlappogram.error.InvalidInversionModeError", false]], "invert() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter.invert", false]], "invert() (overlappogram.inverter method)": [[3, "overlappogram.Inverter.invert", false]], "inverter (class in overlappogram)": [[3, "overlappogram.Inverter", false]], "inverter (class in overlappogram.inversion)": [[4, "overlappogram.inversion.Inverter", false]], "is_inverted (overlappogram.inversion.inverter property)": [[4, "overlappogram.inversion.Inverter.is_inverted", false]], "is_inverted (overlappogram.inverter property)": [[3, "overlappogram.Inverter.is_inverted", false]], "load_overlappogram() (in module overlappogram)": [[3, "overlappogram.load_overlappogram", false]], "load_overlappogram() (in module overlappogram.io)": [[5, "overlappogram.io.load_overlappogram", false]], "load_response_cube() (in module overlappogram)": [[3, "overlappogram.load_response_cube", false]], "load_response_cube() (in module overlappogram.io)": [[5, "overlappogram.io.load_response_cube", false]], "module": [[1, "module-overlappogram.cli", false], [2, "module-overlappogram.error", false], [3, "module-overlappogram", false], [4, "module-overlappogram.inversion", false], [5, "module-overlappogram.io", false], [6, "module-overlappogram.response", false], [7, "module-overlappogram.spectral", false]], "noweightswarnings": [[2, "overlappogram.error.NoWeightsWarnings", false]], "numpy_thread_count (in module overlappogram.cli)": [[1, "overlappogram.cli.NUMPY_THREAD_COUNT", false]], "overlappogram": [[3, "module-overlappogram", false]], "overlappogram.cli": [[1, "module-overlappogram.cli", false]], "overlappogram.error": [[2, "module-overlappogram.error", false]], "overlappogram.inversion": [[4, "module-overlappogram.inversion", false]], "overlappogram.io": [[5, "module-overlappogram.io", false]], "overlappogram.response": [[6, "module-overlappogram.response", false]], "overlappogram.spectral": [[7, "module-overlappogram.spectral", false]], "overlappogramerror": [[2, "overlappogram.error.OverlappogramError", false]], "overlappogramwarning": [[2, "overlappogram.error.OverlappogramWarning", false]], "prepare_response_function() (in module overlappogram.response)": [[6, "overlappogram.response.prepare_response_function", false]], "save_em_cube() (in module overlappogram.io)": [[5, "overlappogram.io.save_em_cube", false]], "save_prediction() (in module overlappogram.io)": [[5, "overlappogram.io.save_prediction", false]], "save_spectral_cube() (in module overlappogram.io)": [[5, "overlappogram.io.save_spectral_cube", false]], "unfold() (in module overlappogram.cli)": [[1, "overlappogram.cli.unfold", false]]}, "objects": {"": [[3, 0, 0, "-", "overlappogram"]], "overlappogram": [[3, 1, 1, "", "Inverter"], [1, 0, 0, "-", "cli"], [2, 0, 0, "-", "error"], [4, 0, 0, "-", "inversion"], [5, 0, 0, "-", "io"], [3, 6, 1, "", "load_overlappogram"], [3, 6, 1, "", "load_response_cube"], [6, 0, 0, "-", "response"], [7, 0, 0, "-", "spectral"]], "overlappogram.Inverter": [[3, 2, 1, "", "_collect_results"], [3, 3, 1, "", "_completed_row_count"], [3, 3, 1, "", "_detector_row_range"], [3, 3, 1, "", "_em_data"], [3, 3, 1, "", "_field_angle_range"], [3, 2, 1, "", "_initialize_with_overlappogram"], [3, 3, 1, "", "_inversion_prediction"], [3, 2, 1, "", "_invert_image_row"], [3, 3, 1, "", "_mode"], [3, 3, 1, "", "_models"], [3, 3, 1, "", "_overlappogram"], [3, 3, 1, "", "_overlappogram_height"], [3, 3, 1, "", "_overlappogram_width"], [3, 3, 1, "", "_progress_bar"], [3, 2, 1, "", "_progress_indicator"], [3, 3, 1, "", "_response_meta"], [3, 3, 1, "", "_row_scores"], [3, 3, 1, "", "_smooth_over"], [3, 3, 1, "", "_solution_fov_width"], [3, 2, 1, "", "_start_chunk_inversion"], [3, 2, 1, "", "_start_row_inversion"], [3, 2, 1, "", "_switch_to_row_inversion"], [3, 3, 1, "", "_thread_count_lock"], [3, 3, 1, "", "_unconverged_rows"], [3, 2, 1, "", "invert"], [3, 4, 1, "", "is_inverted"]], "overlappogram.cli": [[1, 5, 1, "", "NUMPY_THREAD_COUNT"], [1, 6, 1, "", "unfold"]], "overlappogram.error": [[2, 7, 1, "", "InvalidDataFormatError"], [2, 7, 1, "", "InvalidInversionModeError"], [2, 7, 1, "", "NoWeightsWarnings"], [2, 7, 1, "", "OverlappogramError"], [2, 7, 1, "", "OverlappogramWarning"]], "overlappogram.inversion": [[4, 1, 1, "", "Inverter"]], "overlappogram.inversion.Inverter": [[4, 2, 1, "", "_collect_results"], [4, 3, 1, "", "_completed_row_count"], [4, 3, 1, "", "_detector_row_range"], [4, 3, 1, "", "_em_data"], [4, 3, 1, "", "_field_angle_range"], [4, 2, 1, "", "_initialize_with_overlappogram"], [4, 3, 1, "", "_inversion_prediction"], [4, 2, 1, "", "_invert_image_row"], [4, 3, 1, "", "_mode"], [4, 3, 1, "", "_models"], [4, 3, 1, "", "_overlappogram"], [4, 3, 1, "", "_overlappogram_height"], [4, 3, 1, "", "_overlappogram_width"], [4, 3, 1, "", "_progress_bar"], [4, 2, 1, "", "_progress_indicator"], [4, 3, 1, "", "_response_meta"], [4, 3, 1, "", "_row_scores"], [4, 3, 1, "", "_smooth_over"], [4, 3, 1, "", "_solution_fov_width"], [4, 2, 1, "", "_start_chunk_inversion"], [4, 2, 1, "", "_start_row_inversion"], [4, 2, 1, "", "_switch_to_row_inversion"], [4, 3, 1, "", "_thread_count_lock"], [4, 3, 1, "", "_unconverged_rows"], [4, 2, 1, "", "invert"], [4, 4, 1, "", "is_inverted"]], "overlappogram.io": [[5, 6, 1, "", "load_overlappogram"], [5, 6, 1, "", "load_response_cube"], [5, 6, 1, "", "save_em_cube"], [5, 6, 1, "", "save_prediction"], [5, 6, 1, "", "save_spectral_cube"]], "overlappogram.response": [[6, 6, 1, "", "prepare_response_function"]], "overlappogram.spectral": [[7, 6, 1, "", "create_spectrally_pure_images"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "property", "Python property"], "5": ["py", "data", "Python data"], "6": ["py", "function", "Python function"], "7": ["py", "exception", "Python exception"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:property", "5": "py:data", "6": "py:function", "7": "py:exception"}, "terms": {"": [8, 11, 13], "0": [3, 4], "1": [0, 1, 3, 4, 8], "10": 8, "2": [6, 8], "35": 8, "50": [3, 4], "A": 8, "For": 8, "If": [8, 9, 11], "In": [8, 13], "It": [9, 13], "The": [2, 8, 9, 12, 13], "Then": 9, "There": [2, 8, 13], "These": 13, "To": [9, 13], "_collect_result": [3, 4], "_completed_row_count": [3, 4], "_detector_row_rang": [3, 4], "_em_data": [3, 4], "_field_angle_rang": [3, 4], "_initialize_with_overlappogram": [3, 4], "_inversion_predict": [3, 4], "_invert_image_row": [3, 4], "_mode": [3, 4], "_model": [3, 4], "_overlappogram": [3, 4], "_overlappogram_height": [3, 4], "_overlappogram_width": [3, 4], "_progress_bar": [3, 4], "_progress_ind": [3, 4], "_response_meta": [3, 4], "_row_scor": [3, 4], "_smooth_ov": [3, 4], "_solution_fov_width": [3, 4], "_start_chunk_invers": [3, 4], "_start_row_invers": [3, 4], "_switch_to_row_invers": [3, 4], "_thread_count_lock": [3, 4], "_unconverged_row": [3, 4], "about": 13, "accept": 13, "accompani": 8, "accord": 13, "activ": 9, "adjac": 13, "all": [2, 8, 9, 11], "allow": [2, 13], "alpha": [3, 4, 8], "alreadi": 8, "an": [1, 2, 8, 11, 13], "angl": 8, "ani": 9, "api": 12, "appear": 13, "ar": [2, 8, 9, 13], "arc": 8, "artifact": 13, "atom": 8, "auto": 0, "autoapi": 0, "avoid": 13, "background": [12, 13], "base": [2, 9, 13], "becaus": 13, "begin": [8, 13], "benefit": 11, "between": 8, "bin": 9, "bool": [3, 4, 5], "boolean": 8, "boundari": 13, "bug": 11, "build": 12, "built": 9, "can": [8, 9, 11, 13], "captur": 13, "carri": 13, "case": 8, "categori": 2, "check": 9, "chianti": 8, "chunk": 8, "chunk_index": [3, 4], "class": 2, "cli": [0, 3], "code": [9, 11], "coeffici": 8, "combin": 13, "come": 10, "commit": 12, "common": 2, "complet": 13, "comput": 8, "confid": 13, "config": [1, 13], "configur": [1, 12, 13], "consequ": 13, "consist": 9, "constant": 8, "contact": 9, "contain": [0, 8], "contigu": 13, "contribut": 9, "correspond": [8, 13], "could": 13, "cpu": 13, "creat": [0, 9, 13], "create_spectrally_pure_imag": 7, "cube": [5, 13], "cubixss": 12, "current": 8, "cyclic": 8, "data": 2, "default": 8, "defin": [8, 13], "depend": [3, 4, 8], "describ": 8, "descript": 8, "detector": 8, "detector_row_rang": [3, 4, 8], "dev": 9, "develop": 12, "deviat": 8, "differ": 8, "direct": 13, "directori": [8, 9], "discontinu": 13, "discuss": 11, "divid": [8, 13], "do": [8, 9, 13], "doc": 12, "document": [0, 8, 9, 13], "doesn": 13, "done": 13, "e": 9, "each": [8, 13], "eccco": [1, 12], "effect": 8, "either": 8, "elasticnet": [8, 13], "els": 11, "email": 11, "emiss": 13, "encount": 11, "encourag": [9, 11], "environ": 9, "error": [0, 3], "everi": [8, 9], "everyon": 11, "exampl": [8, 12], "execut": [12, 13], "exhaust": 8, "exist": 8, "exit": 2, "expect": 8, "fail": 8, "featur": [8, 13], "few": 13, "fewer": 13, "field": 8, "field_angle_rang": [3, 4, 6, 8], "file": [1, 2, 8, 13], "find": 8, "finish": 13, "first": [9, 11], "five": 8, "float": 8, "follow": 9, "format": [1, 8], "four": 8, "fov_width": 6, "frac": 8, "friendli": 11, "from": [8, 11], "function": 8, "futur": [3, 4], "g": 8, "gener": [0, 13], "get": [9, 13], "github": [1, 11], "given": [1, 13], "gnt": 8, "gnt_path": 7, "ground": 13, "guid": 9, "guidelin": 9, "ha": [2, 8], "happen": 13, "harder": 13, "have": 13, "help": 12, "here": [8, 9], "how": 8, "html": [1, 9], "http": 1, "hybrid": [3, 4, 8], "i": [2, 8, 9, 11, 12, 13], "imag": [8, 13], "image_list": 7, "image_path": [3, 5], "includ": 8, "independ": 13, "index": 12, "indic": 8, "input": 8, "inquiri": 11, "instal": [9, 12], "instead": 13, "instrument": [8, 13], "int": [3, 4], "integ": 8, "invaliddataformaterror": 2, "invalidinversionmodeerror": 2, "invers": [0, 2, 3, 12, 13], "inversionmod": [3, 4], "invert": [3, 4, 8, 12, 13], "io": [0, 1, 3], "is_invert": [3, 4], "issu": [9, 11], "iter": 8, "its": 13, "keyword": 8, "l1_ratio": 8, "learn": 8, "left": 13, "less": 8, "like": [8, 11], "linear": 13, "link": 8, "list": [3, 4, 7, 8], "ll": 9, "load_overlappogram": [3, 5], "load_response_cub": [3, 5], "logarithm": 8, "logt": 8, "loop": 8, "m": 9, "made": 8, "magix": 12, "mai": 13, "make": [8, 9, 11], "make_spectr": 8, "map": 13, "mask": 8, "mask_path": [3, 5], "matrix": 13, "max_it": 8, "maximum": 8, "measur": 13, "method": 8, "mission": 1, "mode": [2, 3, 4, 8, 12], "mode_switch_thread_count": [3, 4, 8, 13], "model": [12, 13], "model_config": [3, 4], "modul": 12, "more": [8, 13], "most": 13, "multipl": 13, "multipli": 8, "multithread": [3, 4], "must": 9, "n": 8, "navig": 9, "ndarrai": [3, 4], "ndcube": [3, 4, 5, 6, 7], "need": [9, 11], "newcom": 13, "next": 13, "non": [2, 13], "none": [3, 4, 5, 6, 7], "note": 8, "notic": [11, 13], "now": [8, 9], "noweightswarn": 2, "num_row_thread": [3, 4], "num_thread": [3, 4, 8, 13], "number": [8, 13], "numpi": [3, 4], "numpy_thread_count": 1, "observ": [12, 13], "omit": 8, "one": 13, "onli": [8, 13], "open": 11, "oper": 8, "optim": [8, 12], "option": 8, "other": [9, 11, 13], "otherwis": 8, "our": 9, "out": 13, "output": [12, 13], "over": 8, "overlap": 13, "overlappogram": [0, 8, 13], "overlappogramerror": 2, "overlappogramwarn": 2, "overview": 12, "overwrit": [5, 8], "overwritten": 8, "own": 13, "packag": [9, 11, 12], "page": [0, 12], "paper": [12, 13], "paramet": [8, 13], "pass": 2, "path": [3, 5, 12], "penalti": 8, "perform": 13, "physic": 8, "pip": [9, 13], "pixel": 8, "pleas": [9, 11], "point": [8, 13], "possibl": [11, 13], "pre": 12, "predict": 5, "prefix": 8, "prepare_response_funct": 6, "prevent": 2, "previou": 13, "process": 2, "program": [8, 13], "progress": [3, 4], "properti": [3, 4, 8], "provid": [8, 12], "pure": [8, 13], "pytest": 9, "python": [9, 12], "r": 9, "random": 8, "rang": 8, "rather": [8, 11], "re": 11, "read": 13, "recommend": [9, 13], "recov": 13, "refer": 12, "regress": 13, "remain": [8, 13], "repositori": 9, "requir": [8, 9], "respons": [0, 3, 8, 13], "response_cub": [3, 4, 6], "response_dependency_list": [3, 4, 6, 8], "response_dependency_nam": 8, "result": 13, "rho": [3, 4, 8], "row": 8, "row_index": [3, 4], "rsp_dep_list": 7, "run": [8, 12], "same": 13, "save_em_cub": 5, "save_predict": 5, "save_spectral_cub": 5, "scikit": 8, "search": 12, "second": 8, "section": [12, 13], "see": [1, 8, 9], "select": 8, "sequenti": [8, 13], "set": [8, 12, 13], "should": 8, "sigma": 8, "simplest": 13, "simpli": 13, "singl": 13, "six": 8, "sklearn": 8, "slitless": 13, "smooth": 8, "smooth_ov": [3, 4, 8], "so": 11, "solut": [8, 13], "solution_fov_width": [3, 4, 8], "some": 13, "someon": 11, "sometim": 13, "soon": 10, "sourc": 9, "speak": 11, "specif": 8, "spectral": [0, 3, 8, 13], "spectral_cub": 5, "spectrogram": 13, "sphinx": [0, 9], "standard": 8, "start": [8, 11, 13], "stop": 13, "str": [3, 4, 5, 7], "string": 8, "style": 9, "suggest": 8, "sun": [12, 13], "support": [8, 11], "switch": [8, 13], "t": [8, 13], "take": 13, "techniqu": 13, "temperatur": 8, "tend": 13, "term": 8, "termin": 13, "test": 12, "than": [8, 11, 13], "thank": 11, "them": 9, "theoret": [12, 13], "thi": [0, 8, 9, 11, 12, 13], "thread": [8, 13], "three": [8, 13], "thu": 13, "time": [9, 13], "tol": 8, "toler": 8, "toml": [1, 8, 13], "too": 11, "track": [3, 4], "train": 8, "true": [5, 8, 13], "truth": 13, "turn": 13, "two": 8, "u": [9, 13], "uncertainti": 8, "understand": 13, "unfold": [1, 2, 8, 13], "unit": 8, "unless": 13, "up": [11, 12], "updat": 8, "us": [3, 4, 8, 9, 11, 13], "user": 11, "util": 13, "valid": 13, "valu": 8, "variou": 8, "venv": 9, "verifi": 13, "view": 8, "virtual": 9, "wai": 13, "wait": 13, "want": 11, "warm": [8, 13], "warm_start": [8, 13], "warn": 2, "we": [8, 9, 11, 13], "weight": [2, 8], "weightless": 8, "weights_path": [3, 5], "what": 8, "when": [8, 9, 13], "where": [8, 13], "whether": 8, "which": 13, "width": 8, "without": 8, "work": [9, 13], "would": [8, 13], "write": 8, "written": 8, "yet": 13, "you": [8, 9, 11, 13], "your": 11}, "titles": ["API Reference", "overlappogram.cli", "overlappogram.error", "overlappogram", "overlappogram.inversion", "overlappogram.io", "overlappogram.response", "overlappogram.spectral", "Configuration", "Development", "Examples", "Help", "Welcome to overlappogram\u2019s documentation!", "Overview"], "titleterms": {"": 12, "api": 0, "attribut": 1, "build": 9, "chunk": 13, "class": [3, 4], "cli": 1, "commit": 9, "configur": 8, "content": [1, 2, 3, 4, 5, 6, 7, 12], "develop": 9, "doc": 9, "document": 12, "error": 2, "exampl": 10, "except": 2, "execut": 8, "function": [1, 3, 5, 6, 7], "help": 11, "hybrid": 13, "indic": 12, "instal": 13, "invers": [4, 8], "io": 5, "mode": 13, "model": 8, "modul": [1, 2, 4, 5, 6, 7], "optim": 13, "output": 8, "overlappogram": [1, 2, 3, 4, 5, 6, 7, 12], "overview": 13, "packag": 3, "path": 8, "pre": 9, "refer": 0, "respons": 6, "row": 13, "run": [9, 13], "section": 8, "set": 9, "spectral": 7, "submodul": 3, "tabl": 12, "test": 9, "up": 9, "welcom": 12}}) \ No newline at end of file +Search.setIndex({"alltitles": {"API Reference": [[0, null]], "Attributes": [[1, "attributes"]], "Building the docs": [[9, "building-the-docs"]], "Chunked mode": [[13, "chunked-mode"]], "Classes": [[3, "classes"], [4, "classes"]], "Configuration": [[8, null]], "Contents:": [[12, null]], "Development": [[9, null]], "Examples": [[10, null]], "Exceptions": [[2, "exceptions"]], "Functions": [[1, "functions"], [3, "functions"], [5, "functions"], [6, "functions"], [7, "functions"]], "Help": [[11, null]], "Hybrid mode": [[13, "hybrid-mode"]], "Indices and tables": [[12, "indices-and-tables"]], "Installation": [[13, "installation"]], "Module Contents": [[1, "module-contents"], [2, "module-contents"], [4, "module-contents"], [5, "module-contents"], [6, "module-contents"], [7, "module-contents"]], "Optimization modes": [[13, "optimization-modes"]], "Overview": [[13, null]], "Package Contents": [[3, "package-contents"]], "Row mode": [[13, "row-mode"]], "Running": [[13, "running"]], "Running tests": [[9, "running-tests"]], "Setting up pre-commit": [[9, "setting-up-pre-commit"]], "Submodules": [[3, "submodules"]], "Welcome to overlappogram\u2019s documentation!": [[12, null]], "execution section": [[8, "execution-section"]], "inversion section": [[8, "inversion-section"]], "model section": [[8, "model-section"]], "output section": [[8, "output-section"]], "overlappogram": [[3, null]], "overlappogram.cli": [[1, null]], "overlappogram.error": [[2, null]], "overlappogram.inversion": [[4, null]], "overlappogram.io": [[5, null]], "overlappogram.response": [[6, null]], "overlappogram.spectral": [[7, null]], "paths section": [[8, "paths-section"]]}, "docnames": ["autoapi/index", "autoapi/overlappogram/cli/index", "autoapi/overlappogram/error/index", "autoapi/overlappogram/index", "autoapi/overlappogram/inversion/index", "autoapi/overlappogram/io/index", "autoapi/overlappogram/response/index", "autoapi/overlappogram/spectral/index", "configuration", "development", "examples", "help", "index", "overview"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2}, "filenames": ["autoapi/index.rst", "autoapi/overlappogram/cli/index.rst", "autoapi/overlappogram/error/index.rst", "autoapi/overlappogram/index.rst", "autoapi/overlappogram/inversion/index.rst", "autoapi/overlappogram/io/index.rst", "autoapi/overlappogram/response/index.rst", "autoapi/overlappogram/spectral/index.rst", "configuration.rst", "development.rst", "examples.rst", "help.rst", "index.rst", "overview.rst"], "indexentries": {"_collect_results() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._collect_results", false]], "_collect_results() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._collect_results", false]], "_completed_row_count (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._completed_row_count", false]], "_completed_row_count (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._completed_row_count", false]], "_detector_row_range (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._detector_row_range", false]], "_detector_row_range (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._detector_row_range", false]], "_em_data (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._em_data", false]], "_em_data (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._em_data", false]], "_field_angle_range (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._field_angle_range", false]], "_field_angle_range (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._field_angle_range", false]], "_initialize_with_overlappogram() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._initialize_with_overlappogram", false]], "_initialize_with_overlappogram() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._initialize_with_overlappogram", false]], "_inversion_prediction (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._inversion_prediction", false]], "_inversion_prediction (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._inversion_prediction", false]], "_invert_image_row() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._invert_image_row", false]], "_invert_image_row() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._invert_image_row", false]], "_mode (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._mode", false]], "_mode (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._mode", false]], "_models (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._models", false]], "_models (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._models", false]], "_n_iter (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._n_iter", false]], "_n_iter (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._n_iter", false]], "_overlappogram (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._overlappogram", false]], "_overlappogram (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._overlappogram", false]], "_overlappogram_height (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._overlappogram_height", false]], "_overlappogram_height (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._overlappogram_height", false]], "_overlappogram_width (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._overlappogram_width", false]], "_overlappogram_width (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._overlappogram_width", false]], "_progress_bar (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._progress_bar", false]], "_progress_bar (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._progress_bar", false]], "_progress_indicator() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._progress_indicator", false]], "_progress_indicator() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._progress_indicator", false]], "_response_meta (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._response_meta", false]], "_response_meta (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._response_meta", false]], "_row_scores (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._row_scores", false]], "_row_scores (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._row_scores", false]], "_smooth_over (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._smooth_over", false]], "_smooth_over (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._smooth_over", false]], "_solution_fov_width (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._solution_fov_width", false]], "_solution_fov_width (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._solution_fov_width", false]], "_start_chunk_inversion() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._start_chunk_inversion", false]], "_start_chunk_inversion() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._start_chunk_inversion", false]], "_start_row_inversion() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._start_row_inversion", false]], "_start_row_inversion() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._start_row_inversion", false]], "_switch_to_row_inversion() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter._switch_to_row_inversion", false]], "_switch_to_row_inversion() (overlappogram.inverter method)": [[3, "overlappogram.Inverter._switch_to_row_inversion", false]], "_thread_count_lock (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._thread_count_lock", false]], "_thread_count_lock (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._thread_count_lock", false]], "_unconverged_rows (overlappogram.inversion.inverter attribute)": [[4, "overlappogram.inversion.Inverter._unconverged_rows", false]], "_unconverged_rows (overlappogram.inverter attribute)": [[3, "overlappogram.Inverter._unconverged_rows", false]], "create_spectrally_pure_images() (in module overlappogram.spectral)": [[7, "overlappogram.spectral.create_spectrally_pure_images", false]], "invaliddataformaterror": [[2, "overlappogram.error.InvalidDataFormatError", false]], "invalidinversionmodeerror": [[2, "overlappogram.error.InvalidInversionModeError", false]], "invert() (overlappogram.inversion.inverter method)": [[4, "overlappogram.inversion.Inverter.invert", false]], "invert() (overlappogram.inverter method)": [[3, "overlappogram.Inverter.invert", false]], "inverter (class in overlappogram)": [[3, "overlappogram.Inverter", false]], "inverter (class in overlappogram.inversion)": [[4, "overlappogram.inversion.Inverter", false]], "is_inverted (overlappogram.inversion.inverter property)": [[4, "overlappogram.inversion.Inverter.is_inverted", false]], "is_inverted (overlappogram.inverter property)": [[3, "overlappogram.Inverter.is_inverted", false]], "load_overlappogram() (in module overlappogram)": [[3, "overlappogram.load_overlappogram", false]], "load_overlappogram() (in module overlappogram.io)": [[5, "overlappogram.io.load_overlappogram", false]], "load_response_cube() (in module overlappogram)": [[3, "overlappogram.load_response_cube", false]], "load_response_cube() (in module overlappogram.io)": [[5, "overlappogram.io.load_response_cube", false]], "module": [[1, "module-overlappogram.cli", false], [2, "module-overlappogram.error", false], [3, "module-overlappogram", false], [4, "module-overlappogram.inversion", false], [5, "module-overlappogram.io", false], [6, "module-overlappogram.response", false], [7, "module-overlappogram.spectral", false]], "noweightswarnings": [[2, "overlappogram.error.NoWeightsWarnings", false]], "numpy_thread_count (in module overlappogram.cli)": [[1, "overlappogram.cli.NUMPY_THREAD_COUNT", false]], "overlappogram": [[3, "module-overlappogram", false]], "overlappogram.cli": [[1, "module-overlappogram.cli", false]], "overlappogram.error": [[2, "module-overlappogram.error", false]], "overlappogram.inversion": [[4, "module-overlappogram.inversion", false]], "overlappogram.io": [[5, "module-overlappogram.io", false]], "overlappogram.response": [[6, "module-overlappogram.response", false]], "overlappogram.spectral": [[7, "module-overlappogram.spectral", false]], "overlappogramerror": [[2, "overlappogram.error.OverlappogramError", false]], "overlappogramwarning": [[2, "overlappogram.error.OverlappogramWarning", false]], "prepare_response_function() (in module overlappogram.response)": [[6, "overlappogram.response.prepare_response_function", false]], "save_em_cube() (in module overlappogram.io)": [[5, "overlappogram.io.save_em_cube", false]], "save_prediction() (in module overlappogram.io)": [[5, "overlappogram.io.save_prediction", false]], "save_spectral_cube() (in module overlappogram.io)": [[5, "overlappogram.io.save_spectral_cube", false]], "unfold() (in module overlappogram.cli)": [[1, "overlappogram.cli.unfold", false]]}, "objects": {"": [[3, 0, 0, "-", "overlappogram"]], "overlappogram": [[3, 1, 1, "", "Inverter"], [1, 0, 0, "-", "cli"], [2, 0, 0, "-", "error"], [4, 0, 0, "-", "inversion"], [5, 0, 0, "-", "io"], [3, 6, 1, "", "load_overlappogram"], [3, 6, 1, "", "load_response_cube"], [6, 0, 0, "-", "response"], [7, 0, 0, "-", "spectral"]], "overlappogram.Inverter": [[3, 2, 1, "", "_collect_results"], [3, 3, 1, "", "_completed_row_count"], [3, 3, 1, "", "_detector_row_range"], [3, 3, 1, "", "_em_data"], [3, 3, 1, "", "_field_angle_range"], [3, 2, 1, "", "_initialize_with_overlappogram"], [3, 3, 1, "", "_inversion_prediction"], [3, 2, 1, "", "_invert_image_row"], [3, 3, 1, "", "_mode"], [3, 3, 1, "", "_models"], [3, 3, 1, "", "_n_iter"], [3, 3, 1, "", "_overlappogram"], [3, 3, 1, "", "_overlappogram_height"], [3, 3, 1, "", "_overlappogram_width"], [3, 3, 1, "", "_progress_bar"], [3, 2, 1, "", "_progress_indicator"], [3, 3, 1, "", "_response_meta"], [3, 3, 1, "", "_row_scores"], [3, 3, 1, "", "_smooth_over"], [3, 3, 1, "", "_solution_fov_width"], [3, 2, 1, "", "_start_chunk_inversion"], [3, 2, 1, "", "_start_row_inversion"], [3, 2, 1, "", "_switch_to_row_inversion"], [3, 3, 1, "", "_thread_count_lock"], [3, 3, 1, "", "_unconverged_rows"], [3, 2, 1, "", "invert"], [3, 4, 1, "", "is_inverted"]], "overlappogram.cli": [[1, 5, 1, "", "NUMPY_THREAD_COUNT"], [1, 6, 1, "", "unfold"]], "overlappogram.error": [[2, 7, 1, "", "InvalidDataFormatError"], [2, 7, 1, "", "InvalidInversionModeError"], [2, 7, 1, "", "NoWeightsWarnings"], [2, 7, 1, "", "OverlappogramError"], [2, 7, 1, "", "OverlappogramWarning"]], "overlappogram.inversion": [[4, 1, 1, "", "Inverter"]], "overlappogram.inversion.Inverter": [[4, 2, 1, "", "_collect_results"], [4, 3, 1, "", "_completed_row_count"], [4, 3, 1, "", "_detector_row_range"], [4, 3, 1, "", "_em_data"], [4, 3, 1, "", "_field_angle_range"], [4, 2, 1, "", "_initialize_with_overlappogram"], [4, 3, 1, "", "_inversion_prediction"], [4, 2, 1, "", "_invert_image_row"], [4, 3, 1, "", "_mode"], [4, 3, 1, "", "_models"], [4, 3, 1, "", "_n_iter"], [4, 3, 1, "", "_overlappogram"], [4, 3, 1, "", "_overlappogram_height"], [4, 3, 1, "", "_overlappogram_width"], [4, 3, 1, "", "_progress_bar"], [4, 2, 1, "", "_progress_indicator"], [4, 3, 1, "", "_response_meta"], [4, 3, 1, "", "_row_scores"], [4, 3, 1, "", "_smooth_over"], [4, 3, 1, "", "_solution_fov_width"], [4, 2, 1, "", "_start_chunk_inversion"], [4, 2, 1, "", "_start_row_inversion"], [4, 2, 1, "", "_switch_to_row_inversion"], [4, 3, 1, "", "_thread_count_lock"], [4, 3, 1, "", "_unconverged_rows"], [4, 2, 1, "", "invert"], [4, 4, 1, "", "is_inverted"]], "overlappogram.io": [[5, 6, 1, "", "load_overlappogram"], [5, 6, 1, "", "load_response_cube"], [5, 6, 1, "", "save_em_cube"], [5, 6, 1, "", "save_prediction"], [5, 6, 1, "", "save_spectral_cube"]], "overlappogram.response": [[6, 6, 1, "", "prepare_response_function"]], "overlappogram.spectral": [[7, 6, 1, "", "create_spectrally_pure_images"]]}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "attribute", "Python attribute"], "4": ["py", "property", "Python property"], "5": ["py", "data", "Python data"], "6": ["py", "function", "Python function"], "7": ["py", "exception", "Python exception"]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:attribute", "4": "py:property", "5": "py:data", "6": "py:function", "7": "py:exception"}, "terms": {"": [8, 11, 13], "0": [3, 4], "1": [0, 1, 3, 4, 8], "10": 8, "2": [6, 8], "35": 8, "50": [3, 4], "A": 8, "For": 8, "If": [8, 9, 11], "In": [8, 13], "It": [9, 13], "The": [2, 8, 9, 12, 13], "Then": 9, "There": [2, 8, 13], "These": 13, "To": [9, 13], "_collect_result": [3, 4], "_completed_row_count": [3, 4], "_detector_row_rang": [3, 4], "_em_data": [3, 4], "_field_angle_rang": [3, 4], "_initialize_with_overlappogram": [3, 4], "_inversion_predict": [3, 4], "_invert_image_row": [3, 4], "_mode": [3, 4], "_model": [3, 4], "_n_iter": [3, 4], "_overlappogram": [3, 4], "_overlappogram_height": [3, 4], "_overlappogram_width": [3, 4], "_progress_bar": [3, 4], "_progress_ind": [3, 4], "_response_meta": [3, 4], "_row_scor": [3, 4], "_smooth_ov": [3, 4], "_solution_fov_width": [3, 4], "_start_chunk_invers": [3, 4], "_start_row_invers": [3, 4], "_switch_to_row_invers": [3, 4], "_thread_count_lock": [3, 4], "_unconverged_row": [3, 4], "about": 13, "accept": 13, "accompani": 8, "accord": 13, "activ": 9, "adjac": 13, "all": [2, 8, 9, 11], "allow": [2, 13], "alpha": [3, 4, 8], "alreadi": 8, "an": [1, 2, 8, 11, 13], "angl": 8, "ani": 9, "api": 12, "appear": 13, "ar": [2, 8, 9, 13], "arc": 8, "artifact": 13, "atom": 8, "auto": 0, "autoapi": 0, "avoid": 13, "background": [12, 13], "base": [2, 9, 13], "becaus": 13, "begin": [8, 13], "benefit": 11, "between": 8, "bin": 9, "bool": [3, 4, 5], "boolean": 8, "boundari": 13, "bug": 11, "build": 12, "built": 9, "can": [8, 9, 11, 13], "captur": 13, "carri": 13, "case": 8, "categori": 2, "check": 9, "chianti": 8, "chunk": 8, "chunk_index": [3, 4], "class": 2, "cli": [0, 3], "code": [9, 11], "coeffici": 8, "combin": 13, "come": 10, "commit": 12, "common": 2, "complet": 13, "comput": 8, "confid": 13, "config": [1, 13], "configur": [1, 12, 13], "consequ": 13, "consist": 9, "constant": 8, "contact": 9, "contain": [0, 8], "contigu": 13, "contribut": 9, "correspond": [8, 13], "could": 13, "cpu": 13, "creat": [0, 9, 13], "create_spectrally_pure_imag": 7, "cube": [5, 13], "cubixss": 12, "current": 8, "cyclic": 8, "data": 2, "default": 8, "defin": [8, 13], "depend": [3, 4, 8], "describ": 8, "descript": 8, "detector": 8, "detector_row_rang": [3, 4, 8], "dev": 9, "develop": 12, "deviat": 8, "differ": 8, "direct": 13, "directori": [8, 9], "discontinu": 13, "discuss": 11, "divid": [8, 13], "do": [8, 9, 13], "doc": 12, "document": [0, 8, 9, 13], "doesn": 13, "done": 13, "e": 9, "each": [8, 13], "eccco": [1, 12], "effect": 8, "either": 8, "elasticnet": [8, 13], "els": 11, "email": 11, "emiss": 13, "encount": 11, "encourag": [9, 11], "environ": 9, "error": [0, 3], "everi": [8, 9], "everyon": 11, "exampl": [8, 12], "execut": [12, 13], "exhaust": 8, "exist": 8, "exit": 2, "expect": 8, "fail": 8, "featur": [8, 13], "few": 13, "fewer": 13, "field": 8, "field_angle_rang": [3, 4, 6, 8], "file": [1, 2, 8, 13], "find": 8, "finish": 13, "first": [9, 11], "five": 8, "float": 8, "follow": 9, "format": [1, 8], "four": 8, "fov_width": 6, "frac": 8, "friendli": 11, "from": [8, 11], "function": 8, "futur": [3, 4], "g": 8, "gener": [0, 13], "get": [9, 13], "github": [1, 11], "given": [1, 13], "gnt": 8, "gnt_path": 7, "ground": 13, "guid": 9, "guidelin": 9, "ha": [2, 8], "happen": 13, "harder": 13, "have": 13, "help": 12, "here": [8, 9], "how": 8, "html": [1, 9], "http": 1, "hybrid": [3, 4, 8], "i": [2, 8, 9, 11, 12, 13], "imag": [8, 13], "image_list": 7, "image_path": [3, 5], "includ": 8, "independ": 13, "index": 12, "indic": 8, "input": 8, "inquiri": 11, "instal": [9, 12], "instead": 13, "instrument": [8, 13], "int": [3, 4], "integ": 8, "invaliddataformaterror": 2, "invalidinversionmodeerror": 2, "invers": [0, 2, 3, 12, 13], "inversionmod": [3, 4], "invert": [3, 4, 8, 12, 13], "io": [0, 1, 3], "is_invert": [3, 4], "issu": [9, 11], "iter": 8, "its": 13, "keyword": 8, "l1_ratio": 8, "learn": 8, "left": 13, "less": 8, "like": [8, 11], "linear": 13, "link": 8, "list": [3, 4, 7, 8], "ll": 9, "load_overlappogram": [3, 5], "load_response_cub": [3, 5], "logarithm": 8, "logt": 8, "loop": 8, "m": 9, "made": 8, "magix": 12, "mai": 13, "make": [8, 9, 11], "make_spectr": 8, "map": 13, "mask": 8, "mask_path": [3, 5], "matrix": 13, "max_it": 8, "maximum": 8, "measur": 13, "method": 8, "mission": 1, "mode": [2, 3, 4, 8, 12], "mode_switch_thread_count": [3, 4, 8, 13], "model": [12, 13], "model_config": [3, 4], "modul": 12, "more": [8, 13], "most": 13, "multipl": 13, "multipli": 8, "multithread": [3, 4], "must": 9, "n": 8, "navig": 9, "ndarrai": [3, 4], "ndcube": [3, 4, 5, 6, 7], "need": [9, 11], "newcom": 13, "next": 13, "non": [2, 13], "none": [3, 4, 5, 6, 7], "note": 8, "notic": [11, 13], "now": [8, 9], "noweightswarn": 2, "num_row_thread": [3, 4], "num_thread": [3, 4, 8, 13], "number": [8, 13], "numpi": [3, 4], "numpy_thread_count": 1, "observ": [12, 13], "omit": 8, "one": 13, "onli": [8, 13], "open": 11, "oper": 8, "optim": [8, 12], "option": 8, "other": [9, 11, 13], "otherwis": 8, "our": 9, "out": 13, "output": [12, 13], "over": 8, "overlap": 13, "overlappogram": [0, 8, 13], "overlappogramerror": 2, "overlappogramwarn": 2, "overview": 12, "overwrit": [5, 8], "overwritten": 8, "own": 13, "packag": [9, 11, 12], "page": [0, 12], "paper": [12, 13], "paramet": [8, 13], "pass": 2, "path": [3, 5, 12], "penalti": 8, "perform": 13, "physic": 8, "pip": [9, 13], "pixel": 8, "pleas": [9, 11], "point": [8, 13], "possibl": [11, 13], "pre": 12, "predict": 5, "prefix": 8, "prepare_response_funct": 6, "prevent": 2, "previou": 13, "process": 2, "program": [8, 13], "progress": [3, 4], "properti": [3, 4, 8], "provid": [8, 12], "pure": [8, 13], "pytest": 9, "python": [9, 12], "r": 9, "random": 8, "rang": 8, "rather": [8, 11], "re": 11, "read": 13, "recommend": [9, 13], "recov": 13, "refer": 12, "regress": 13, "remain": [8, 13], "repositori": 9, "requir": [8, 9], "respons": [0, 3, 8, 13], "response_cub": [3, 4, 6], "response_dependency_list": [3, 4, 6, 8], "response_dependency_nam": 8, "result": 13, "rho": [3, 4, 8], "row": 8, "row_index": [3, 4], "rsp_dep_list": 7, "run": [8, 12], "same": 13, "save_em_cub": 5, "save_predict": 5, "save_spectral_cub": 5, "scikit": 8, "search": 12, "second": 8, "section": [12, 13], "see": [1, 8, 9], "select": 8, "sequenti": [8, 13], "set": [8, 12, 13], "should": 8, "sigma": 8, "simplest": 13, "simpli": 13, "singl": 13, "six": 8, "sklearn": 8, "slitless": 13, "smooth": 8, "smooth_ov": [3, 4, 8], "so": 11, "solut": [8, 13], "solution_fov_width": [3, 4, 8], "some": 13, "someon": 11, "sometim": 13, "soon": 10, "sourc": 9, "speak": 11, "specif": 8, "spectral": [0, 3, 8, 13], "spectral_cub": 5, "spectrogram": 13, "sphinx": [0, 9], "standard": 8, "start": [8, 11, 13], "stop": 13, "str": [3, 4, 5, 7], "string": 8, "style": 9, "suggest": 8, "sun": [12, 13], "support": [8, 11], "switch": [8, 13], "t": [8, 13], "take": 13, "techniqu": 13, "temperatur": 8, "tend": 13, "term": 8, "termin": 13, "test": 12, "than": [8, 11, 13], "thank": 11, "them": 9, "theoret": [12, 13], "thi": [0, 8, 9, 11, 12, 13], "thread": [8, 13], "three": [8, 13], "thu": 13, "time": [9, 13], "tol": 8, "toler": 8, "toml": [1, 8, 13], "too": 11, "track": [3, 4], "train": 8, "true": [5, 8, 13], "truth": 13, "turn": 13, "two": 8, "u": [9, 13], "uncertainti": 8, "understand": 13, "unfold": [1, 2, 8, 13], "unit": 8, "unless": 13, "up": [11, 12], "updat": 8, "us": [3, 4, 8, 9, 11, 13], "user": 11, "util": 13, "valid": 13, "valu": 8, "variou": 8, "venv": 9, "verifi": 13, "view": 8, "virtual": 9, "wai": 13, "wait": 13, "want": 11, "warm": [8, 13], "warm_start": [8, 13], "warn": 2, "we": [8, 9, 11, 13], "weight": [2, 8], "weightless": 8, "weights_path": [3, 5], "what": 8, "when": [8, 9, 13], "where": [8, 13], "whether": 8, "which": 13, "width": 8, "without": 8, "work": [9, 13], "would": [8, 13], "write": 8, "written": 8, "yet": 13, "you": [8, 9, 11, 13], "your": 11}, "titles": ["API Reference", "overlappogram.cli", "overlappogram.error", "overlappogram", "overlappogram.inversion", "overlappogram.io", "overlappogram.response", "overlappogram.spectral", "Configuration", "Development", "Examples", "Help", "Welcome to overlappogram\u2019s documentation!", "Overview"], "titleterms": {"": 12, "api": 0, "attribut": 1, "build": 9, "chunk": 13, "class": [3, 4], "cli": 1, "commit": 9, "configur": 8, "content": [1, 2, 3, 4, 5, 6, 7, 12], "develop": 9, "doc": 9, "document": 12, "error": 2, "exampl": 10, "except": 2, "execut": 8, "function": [1, 3, 5, 6, 7], "help": 11, "hybrid": 13, "indic": 12, "instal": 13, "invers": [4, 8], "io": 5, "mode": 13, "model": 8, "modul": [1, 2, 4, 5, 6, 7], "optim": 13, "output": 8, "overlappogram": [1, 2, 3, 4, 5, 6, 7, 12], "overview": 13, "packag": 3, "path": 8, "pre": 9, "refer": 0, "respons": 6, "row": 13, "run": [9, 13], "section": 8, "set": 9, "spectral": 7, "submodul": 3, "tabl": 12, "test": 9, "up": 9, "welcom": 12}}) \ No newline at end of file