gammapy__gammapy-5674

{
  "status": "ok",
  "stdout": "840:    def resample_axis(self, axis_new):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "31:def squash_fluxpoints(flux_point, axis):\n869:            fp_new = squash_fluxpoints(fp, axis_new)\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "gammapy/estimators/points/core.py",
  "content": "\ndef squash_fluxpoints(flux_point, axis):\n    \"\"\"Squash a `~FluxPoints` object into one point.\n\n    The log-likelihoods profiles in each bin are summed\n    to compute the resultant quantities. Stat profiles\n    must be present on the `~FluxPoints` object for\n    this method to work.\n    \"\"\"\n    value_scan = flux_point.stat_scan.geom.axes[\"norm\"].center\n    stat_scan = np.sum(flux_point.stat_scan.data, axis=0).ravel()\n    f = interp1d(value_scan, stat_scan, kind=\"quadratic\", bounds_error=False)\n    f = interpolate_profile(value_scan, stat_scan)\n    minimizer = minimize(\n        f,\n        x0=value_scan[int(len(value_scan) / 2)],\n        bounds=[(value_scan[0], value_scan[-1])],\n        method=\"L-BFGS-B\",\n    )\n\n    maps = Maps()\n    geom = flux_point.geom.to_image()\n    if axis.name != \"energy\":\n        geom = geom.to_cube([flux_point.geom.axes[\"energy\"]])\n\n    maps[\"norm\"] = Map.from_geom(geom, data=minimizer.x)\n    maps[\"norm_err\"] = Map.from_geom(\n        geom, data=np.sqrt(minimizer.hess_inv.todense()).reshape(geom.data_shape)\n    )\n    maps[\"n_dof\"] = Map.from_geom(geom, data=flux_point.geom.axes[axis.name].nbin)\n\n    if \"norm_ul\" in flux_point.available_quantities:\n        delta_ts = flux_point.meta.get(\"n_sigma_ul\", 2) ** 2\n        ul = stat_profile_ul_scipy(value_scan, stat_scan, delta_ts=delta_ts)\n        maps[\"norm_ul\"] = Map.from_geom(geom, data=ul.value)\n\n    maps[\"stat\"] = Map.from_geom(geom, data=f(minimizer.x))\n\n    geom_scan = geom.to_cube([MapAxis.from_nodes(value_scan, name=\"norm\")])\n    maps[\"stat_scan\"] = Map.from_geom(\n        geom=geom_scan, data=stat_scan.reshape(geom_scan.data_shape)\n    )\n    try:\n        maps[\"stat_null\"] = Map.from_geom(geom, data=np.sum(flux_point.stat_null.data))\n        maps[\"ts\"] = maps[\"stat_null\"] - maps[\"stat\"]\n    except AttributeError:\n        log.info(\n            \"Stat null info not present on original FluxPoints object. TS not computed\"\n        )\n\n    maps[\"success\"] = Map.from_geom(geom=geom, data=minimizer.success, dtype=bool)\n\n    combined_fp = FluxPoints.from_maps(\n        maps=maps,\n        sed_type=flux_point.sed_type_init,\n        reference_model=flux_point.reference_model,\n        gti=flux_point.gti,\n        meta=flux_point.meta,\n    )\n    return combined_fp\n\n\nclass FluxPoints(FluxMaps):\n    \"\"\"Flux points container.\n\n    The supported formats are described here: :ref:`gadf:flux-points`.\n\n    In summary, the following formats and minimum required columns are:\n\n    * Format ``dnde``: columns ``e_ref`` and ``dnde``\n    * Format ``e2dnde``: columns ``e_ref``, ``e2dnde``",
  "start_line": 30,
  "end_line": 100,
  "total_lines": 872,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "gammapy/estimators/points/core.py",
  "content": "    def resample_axis(self, axis_new):\n        \"\"\"Rebin the flux point object along the new axis.\n\n        The log-likelihoods profiles in each bin are summed\n        to compute the resultant quantities.\n        Stat profiles must be present on the `~gammapy.estimators.FluxPoints` object for\n        this method to work.\n\n        For now, works only for flat `~gammapy.estimators.FluxPoints`.\n\n        Parameters\n        ----------\n        axis_new : `MapAxis` or `TimeMapAxis`\n            The new axis to resample along\n\n        Returns\n        -------\n        flux_points : `~gammapy.estimators.FluxPoints`\n            A new FluxPoints object with modified axis.\n        \"\"\"\n        if not self.has_stat_profiles:\n            raise ValueError(\"Stat profiles not present, rebinning is not possible\")\n\n        fluxpoints = []\n        for edge_min, edge_max in zip(axis_new.edges_min, axis_new.edges_max):\n            if isinstance(axis_new, TimeMapAxis):\n                edge_min = edge_min + axis_new.reference_time\n                edge_max = edge_max + axis_new.reference_time\n            fp = self.slice_by_coord({axis_new.name: slice(edge_min, edge_max)})\n            fp_new = squash_fluxpoints(fp, axis_new)\n            fluxpoints.append(fp_new)\n\n        return self.__class__.from_stack(fluxpoints, axis=axis_new)",
  "start_line": 840,
  "end_line": 872,
  "total_lines": 872,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "stdout": "__init__.py\ntest_core.py\ntest_energydependentmorphology.py\ntest_flux.py\ntest_metadata.py\ntest_parameter_estimator.py\ntest_profile.py\ntest_utils.py\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "Traceback (most recent call last):\n  File \"<stdin>\", line 3, in <module>\nImportError: cannot import name 'Geometry' from 'gammapy.maps' (/workspace/gammapy/maps/__init__.py)\n",
  "details": {
    "stdout": "",
    "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 3, in <module>\nImportError: cannot import name 'Geometry' from 'gammapy.maps' (/workspace/gammapy/maps/__init__.py)\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "filepath": "gammapy/maps/__init__.py",
  "content": "# Licensed under a 3-clause BSD style license - see LICENSE.rst\n\"\"\"Sky maps.\"\"\"\nfrom .axes import LabelMapAxis, MapAxes, MapAxis, TimeMapAxis\nfrom .coord import MapCoord\nfrom .core import Map\nfrom .geom import Geom\nfrom .hpx import HpxGeom, HpxMap, HpxNDMap\nfrom .maps import Maps\nfrom .measure import containment_radius, containment_region\nfrom .region import RegionGeom, RegionNDMap\nfrom .wcs import WcsGeom, WcsMap, WcsNDMap\n\n__all__ = [\n    \"Geom\",\n    \"HpxGeom\",\n    \"HpxMap\",\n    \"HpxNDMap\",\n    \"LabelMapAxis\",\n    \"Map\",\n    \"MapAxes\",\n    \"MapAxis\",\n    \"MapCoord\",\n    \"Maps\",\n    \"RegionGeom\",\n    \"RegionNDMap\",\n    \"TimeMapAxis\",\n    \"WcsGeom\",\n    \"WcsMap\",\n    \"WcsNDMap\",\n    \"containment_radius\",\n    \"containment_region\",\n]",
  "start_line": 1,
  "end_line": 32,
  "total_lines": 32,
  "is_truncated": false
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "Traceback (most recent call last):\n  File \"<stdin>\", line 4, in <module>\n  File \"/workspace/gammapy/estimators/__init__.py\", line 4, in <module>\n    from .core import Estimator\n  File \"/workspace/gammapy/estimators/core.py\", line 9, in <module>\n    from gammapy.modeling.models import ModelBase\n  File \"/workspace/gammapy/modeling/__init__.py\", line 8, in <module>\n    from .selection import select_nested_models\n  File \"/workspace/gammapy/modeling/selection.py\", line 4, in <module>\n    from gammapy.stats.utils import sigma_to_ts\n  File \"/workspace/gammapy/stats/__init__.py\", line 4, in <module>\n    from .counts_statistic import CashCountsStatistic, WStatCountsStatistic\n  File \"/workspace/gammapy/stats/counts_statistic.py\", line 8, in <module>\n    from .fit_statistics import cash, wstat\n  File \"/workspace/gammapy/stats/fit_statistics.py\", line 8, in <module>\n    from gammapy.stats.fit_statistics_cython import TRUNCATION_VALUE\nModuleNotFoundError: No module named 'gammapy.stats.fit_statistics_cython'\n",
  "details": {
    "stdout": "",
    "stderr": "Traceback (most recent call last):\n  File \"<stdin>\", line 4, in <module>\n  File \"/workspace/gammapy/estimators/__init__.py\", line 4, in <module>\n    from .core import Estimator\n  File \"/workspace/gammapy/estimators/core.py\", line 9, in <module>\n    from gammapy.modeling.models import ModelBase\n  File \"/workspace/gammapy/modeling/__init__.py\", line 8, in <module>\n    from .selection import select_nested_models\n  File \"/workspace/gammapy/modeling/selection.py\", line 4, in <module>\n    from gammapy.stats.utils import sigma_to_ts\n  File \"/workspace/gammapy/stats/__init__.py\", line 4, in <module>\n    from .counts_statistic import CashCountsStatistic, WStatCountsStatistic\n  File \"/workspace/gammapy/stats/counts_statistic.py\", line 8, in <module>\n    from .fit_statistics import cash, wstat\n  File \"/workspace/gammapy/stats/fit_statistics.py\", line 8, in <module>\n    from gammapy.stats.fit_statistics_cython import TRUNCATION_VALUE\nModuleNotFoundError: No module named 'gammapy.stats.fit_statistics_cython'\n",
    "exit_code": 1
  }
}

{
  "status": "ok",
  "stdout": "/workspace/gammapy/stats/fit_statistics_cython.pyx\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "In /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nImportError while loading conftest '/workspace/gammapy/conftest.py'.\n/gammapy/gammapy/conftest.py:12: in <module>\n    from gammapy.data import GTI\n/gammapy/gammapy/data/__init__.py:4: in <module>\n    from .data_store import DataStore\n/gammapy/gammapy/data/data_store.py:17: in <module>\n    from .observations import Observation, ObservationChecker, Observations\n/gammapy/gammapy/data/observations.py:20: in <module>\n    from gammapy.utils.metadata import CreatorMetaData, TargetMetaData, TimeInfoMetaData\n/gammapy/gammapy/utils/metadata.py:16: in <module>\n    from gammapy.version import version\nE   ModuleNotFoundError: No module named 'gammapy.version'\n",
  "details": {
    "stdout": "",
    "stderr": "In /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'parseString' deprecated - use 'parse_string'\nIn /usr/local/lib/python3.10/site-packages/matplotlib/mpl-data/stylelib/classic.mplstyle: 'resetCache' deprecated - use 'reset_cache'\nImportError while loading conftest '/workspace/gammapy/conftest.py'.\n/gammapy/gammapy/conftest.py:12: in <module>\n    from gammapy.data import GTI\n/gammapy/gammapy/data/__init__.py:4: in <module>\n    from .data_store import DataStore\n/gammapy/gammapy/data/data_store.py:17: in <module>\n    from .observations import Observation, ObservationChecker, Observations\n/gammapy/gammapy/data/observations.py:20: in <module>\n    from gammapy.utils.metadata import CreatorMetaData, TargetMetaData, TimeInfoMetaData\n/gammapy/gammapy/utils/metadata.py:16: in <module>\n    from gammapy.version import version\nE   ModuleNotFoundError: No module named 'gammapy.version'\n",
    "exit_code": 4
  }
}

{
  "status": "error",
  "error_type": "CommandError",
  "error_message": "ls: cannot access 'gammapy/version.py': No such file or directory\n",
  "details": {
    "stdout": "",
    "stderr": "ls: cannot access 'gammapy/version.py': No such file or directory\n",
    "exit_code": 2
  }
}

{
  "status": "ok",
  "filepath": "gammapy/maps/core.py",
  "content": "        from .hpx import HpxGeom\n        from .region import RegionGeom\n        from .wcs import WcsGeom\n\n        if isinstance(geom, HpxGeom):\n            map_type = \"hpx\"\n        elif isinstance(geom, WcsGeom):\n            map_type = \"wcs\"\n        elif isinstance(geom, RegionGeom):\n            map_type = \"region\"\n        else:\n            raise ValueError(\"Unrecognized geom type.\")\n\n        cls_out = Map._get_map_cls(map_type)\n        return cls_out(geom, data=data, meta=meta, unit=unit, dtype=dtype)\n\n    @staticmethod\n    def from_hdulist(\n        hdulist, hdu=None, hdu_bands=None, map_type=\"auto\", format=None, colname=None\n    ):\n        \"\"\"Create from a `astropy.io.fits.HDUList` object.",
  "start_line": 290,
  "end_line": 310,
  "total_lines": 2109,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "gammapy/maps/region/ndmap.py",
  "content": "            data = np.zeros(geom.data_shape, dtype=dtype)\n\n        if meta is None:\n            meta = {}\n\n        self._geom = geom\n        self.data = data\n        self.meta = meta\n        self._unit = u.Unit(unit)\n\n    @property\n    def data(self):\n        return self._data\n\n    @data.setter\n    def data(self, value):\n        \"\"\"Set data.\n        Parameters\n        ----------\n        value : array-like\n            Data array.\n        \"\"\"\n        if np.isscalar(value):\n            value = value * np.ones(self.geom.data_shape, dtype=type(value))\n\n        if isinstance(value, u.Quantity):\n            raise TypeError(\"Map data must be a Numpy array. Set unit separately\")\n\n        input_shape = value.shape\n        if len(self.geom.data_shape) == 2 + len(value.shape):\n            if self.geom.data_shape[: len(value.shape)] == value.shape:\n                value = np.expand_dims(value, (-2, -1))\n\n        if self.geom.data_shape != value.shape:\n            raise ValueError(\n                f\"Input shape {input_shape} is not compatible with shape from geometry {self.geom.data_shape}\"\n            )\n\n        self._data = value\n\n    def plot(self, ax=None, axis_name=None, **kwargs):\n        \"\"\"Plot the data contained in region map along the non-spatial axis.\n\n        Parameters\n        ----------\n        ax : `~matplotlib.pyplot.Axis`, optional\n            Axis used for plotting.\n            Default is None.\n        axis_name : str, optional\n            Which axis to plot on the x-axis. Extra axes will be plotted as\n            additional lines. Default is None.",
  "start_line": 50,
  "end_line": 100,
  "total_lines": 837,
  "is_truncated": false
}

{
  "status": "ok",
  "filepath": "gammapy/estimators/points/core.py",
  "content": "        reference_model : `SpectralModel`, optional\n            Reference spectral model. Default is None.\n        gti : `GTI`, optional\n            Good time intervals. Default is None.\n\n        Returns\n        -------\n        flux_points : `FluxPoints`\n            Flux points.\n        \"\"\"\n        table = table_standardise_units_copy(table)\n\n        if format is None:\n            format = cls._table_guess_format(table)\n            log.info(\"Inferred format: \" + format)\n\n        if sed_type is None:\n            sed_type = table.meta.get(\"SED_TYPE\", None)\n\n        if sed_type is None:\n            sed_type = cls._guess_sed_type(table.colnames)\n\n        if sed_type is None:\n            raise ValueError(\"Specifying the SED type is required\")\n\n        if sed_type == \"likelihood\":\n            table = cls._convert_loglike_columns(table)\n            if reference_model is None:\n                reference_model = TemplateSpectralModel(\n                    energy=flat_if_equal(table[\"e_ref\"].quantity),\n                    values=flat_if_equal(table[\"ref_dnde\"].quantity),\n                )\n\n        maps = Maps()\n        table.meta.setdefault(\"SED_TYPE\", sed_type)\n\n        for name in cls.all_quantities(sed_type=sed_type):\n            if name in table.colnames:\n                maps[name] = RegionNDMap.from_table(\n                    table=table, colname=name, format=format\n                )\n\n        meta = cls._get_meta_gadf(table)\n        return cls.from_maps(\n            maps=maps,\n            reference_model=reference_model,\n            meta=meta,\n            sed_type=sed_type,\n            gti=gti,\n        )\n",
  "start_line": 330,
  "end_line": 380,
  "total_lines": 872,
  "is_truncated": false
}

{
  "status": "ok",
  "stdout": "31:def squash_fluxpoints(flux_point, axis):\n",
  "stderr": "",
  "exit_code": 0
}

{
  "status": "ok",
  "filepath": "gammapy/estimators/points/core.py",
  "content": "def squash_fluxpoints(flux_point, axis):\n    \"\"\"Squash a `~FluxPoints` object into one point.\n\n    The log-likelihoods profiles in each bin are summed\n    to compute the resultant quantities. Stat profiles\n    must be present on the `~FluxPoints` object for\n    this method to work.\n    \"\"\"\n    value_scan = flux_point.stat_scan.geom.axes[\"norm\"].center\n    stat_scan = np.sum(flux_point.stat_scan.data, axis=0).ravel()\n    f = interp1d(value_scan, stat_scan, kind=\"quadratic\", bounds_error=False)\n    f = interpolate_profile(value_scan, stat_scan)\n    minimizer = minimize(\n        f,\n        x0=value_scan[int(len(value_scan) / 2)],\n        bounds=[(value_scan[0], value_scan[-1])],\n        method=\"L-BFGS-B\",\n    )\n\n    maps = Maps()\n    geom = flux_point.geom.to_image()\n    if axis.name != \"energy\":\n        geom = geom.to_cube([flux_point.geom.axes[\"energy\"]])\n\n    maps[\"norm\"] = Map.from_geom(geom, data=minimizer.x)\n    maps[\"norm_err\"] = Map.from_geom(\n        geom, data=np.sqrt(minimizer.hess_inv.todense()).reshape(geom.data_shape)\n    )\n    maps[\"n_dof\"] = Map.from_geom(geom, data=flux_point.geom.axes[axis.name].nbin)\n\n    if \"norm_ul\" in flux_point.available_quantities:\n        delta_ts = flux_point.meta.get(\"n_sigma_ul\", 2) ** 2\n        ul = stat_profile_ul_scipy(value_scan, stat_scan, delta_ts=delta_ts)\n        maps[\"norm_ul\"] = Map.from_geom(geom, data=ul.value)\n\n    maps[\"stat\"] = Map.from_geom(geom, data=f(minimizer.x))\n\n    geom_scan = geom.to_cube([MapAxis.from_nodes(value_scan, name=\"norm\")])\n    maps[\"stat_scan\"] = Map.from_geom(\n        geom=geom_scan, data=stat_scan.reshape(geom_scan.data_shape)\n    )\n    try:\n        maps[\"stat_null\"] = Map.from_geom(geom, data=np.sum(flux_point.stat_null.data))\n        maps[\"ts\"] = maps[\"stat_null\"] - maps[\"stat\"]\n    except AttributeError:\n        log.info(\n            \"Stat null info not present on original FluxPoints object. TS not computed\"\n        )\n\n    maps[\"success\"] = Map.from_geom(geom=geom, data=minimizer.success, dtype=bool)",
  "start_line": 31,
  "end_line": 80,
  "total_lines": 872,
  "is_truncated": false
}