onnx-diagnostic 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

onnx_diagnostic/helpers/log_helper.py

@@ -0,0 +1,585 @@
+import datetime
+import glob
+import os
+import re
+import zipfile
+from typing import Any, Callable, Dict, Iterator, List, Optional, Sequence, Tuple, Union
+import numpy as np
+import pandas
+from pandas.api.types import is_numeric_dtype
+from .helper import string_sig
+
+
+def enumerate_csv_files(
+    data: Union[
+        pandas.DataFrame, List[Union[str, Tuple[str, str]]], str, Tuple[str, str, str, str]
+    ],
+    verbose: int = 0,
+) -> Iterator[Union[pandas.DataFrame, str, Tuple[str, str, str, str]]]:
+    """
+    Enumerates files considered for the aggregation.
+    Only csv files are considered.
+    If a zip file is given, the function digs into the zip files and
+    loops over csv candidates.
+
+    :param data: dataframe with the raw data or a file or list of files
+
+    data can contains:
+    * a dataframe
+    * a string for a filename, zip or csv
+    * a list of string
+    * a tuple
+    """
+    if not isinstance(data, list):
+        data = [data]
+    for itn, filename in enumerate(data):
+        if isinstance(filename, pandas.DataFrame):
+            if verbose:
+                print(f"[enumerate_csv_files] data[{itn}] is a dataframe")
+            yield filename
+            continue
+
+        if isinstance(filename, tuple):
+            # A file in a zipfile
+            if verbose:
+                print(f"[enumerate_csv_files] data[{itn}] is {filename!r}")
+            yield filename
+            continue
+
+        if os.path.exists(filename):
+            ext = os.path.splitext(filename)[-1]
+            if ext == ".csv":
+                # We check the first line is ok.
+                if verbose:
+                    print(f"[enumerate_csv_files] data[{itn}] is a csv file: {filename!r}]")
+                with open(filename, "r", encoding="utf-8") as f:
+                    line = f.readline()
+                    if "~help" in line or (",CMD" not in line and ",DATE" not in line):
+                        continue
+                    dt = datetime.datetime.fromtimestamp(os.stat(filename).st_mtime)
+                    du = dt.strftime("%Y-%m-%d %H:%M:%S")
+                    yield (os.path.split(filename)[-1], du, filename, "")
+                continue
+
+            if ext == ".zip":
+                if verbose:
+                    print(f"[enumerate_csv_files] data[{itn}] is a zip file: {filename!r}]")
+                zf = zipfile.ZipFile(filename, "r")
+                for ii, info in enumerate(zf.infolist()):
+                    name = info.filename
+                    ext = os.path.splitext(name)[-1]
+                    if ext != ".csv":
+                        continue
+                    if verbose:
+                        print(
+                            f"[enumerate_csv_files] data[{itn}][{ii}] is a csv file: {name!r}]"
+                        )
+                    with zf.open(name) as zzf:
+                        first_line = zzf.readline()
+                    if b"," not in first_line:
+                        continue
+                    yield (
+                        os.path.split(name)[-1],
+                        "%04d-%02d-%02d %02d:%02d:%02d" % info.date_time,
+                        name,
+                        filename,
+                    )
+                zf.close()
+                continue
+
+            raise AssertionError(f"Unexpected format {filename!r}, cannot read it.")
+
+        # filename is a pattern.
+        found = glob.glob(filename)
+        if verbose and not found:
+            print(f"[enumerate_csv_files] unable to find file in {filename!r}")
+        for ii, f in enumerate(found):
+            if verbose:
+                print(f"[enumerate_csv_files] data[{itn}][{ii}] {f!r} from {filename!r}")
+            yield from enumerate_csv_files(f, verbose=verbose)
+
+
+def open_dataframe(
+    data: Union[str, Tuple[str, str, str, str], pandas.DataFrame],
+) -> pandas.DataFrame:
+    """
+    Opens a filename.
+
+    :param data: a dataframe, a filename, a tuple indicating the file is coming
+        from a zip file
+    :return: a dataframe
+    """
+    if isinstance(data, pandas.DataFrame):
+        return data
+    if isinstance(data, str):
+        df = pandas.read_csv(data)
+        df["RAWFILENAME"] = data
+        return df
+    if isinstance(data, tuple):
+        if not data[-1]:
+            df = pandas.read_csv(data[2])
+            df["RAWFILENAME"] = data[2]
+            return df
+        zf = zipfile.ZipFile(data[-1])
+        with zf.open(data[2]) as f:
+            df = pandas.read_csv(f)
+            df["RAWFILENAME"] = f"{data[-1]}/{data[2]}"
+        zf.close()
+        return df
+
+    raise ValueError(f"Unexpected value for data: {data!r}")
+
+
+class CubeViewDef:
+    """
+    Defines how to compute a view.
+
+    :param key_index: keys to put in the row index
+    :param values: values to show
+    :param ignore_unique: ignore keys with a unique value
+    :param order: to reorder key in columns index
+    :param key_agg: aggregate according to these columns before
+        creating the view
+    :param agg_args: see :meth:`pandas.core.groupby.DataFrameGroupBy.agg`
+    :param agg_kwargs: see :meth:`pandas.core.groupby.DataFrameGroupBy.agg`
+    """
+
+    def __init__(
+        self,
+        key_index: Sequence[str],
+        values: Sequence[str],
+        ignore_unique: bool = True,
+        order: Optional[Sequence[str]] = None,
+        key_agg: Optional[Sequence[str]] = None,
+        agg_args: Sequence[Any] = ("sum",),
+        agg_kwargs: Optional[Dict[str, Any]] = None,
+    ):
+        self.key_index = key_index
+        self.values = values
+        self.ignore_unique = ignore_unique
+        self.order = order
+        self.key_agg = key_agg
+        self.agg_args = agg_args
+        self.agg_kwargs = agg_kwargs
+
+    def __repr__(self) -> str:
+        "usual"
+        return string_sig(self)  # type: ignore[arg-type]
+
+
+class CubeLogs:
+    """
+    Processes logs coming from experiments.
+    """
+
+    def __init__(
+        self,
+        data: Any,
+        time: str = "date",
+        keys: Sequence[str] = ("version_.*", "model_.*"),
+        values: Sequence[str] = ("time_.*", "disc_.*"),
+        ignored: Sequence[str] = (),
+        recent: bool = False,
+        formulas: Optional[Dict[str, Callable[[pandas.DataFrame], pandas.Series]]] = None,
+    ):
+        self._data = data
+        self._time = time
+        self._keys = keys
+        self._values = values
+        self._ignored = ignored
+        self.recent = recent
+        self._formulas = formulas
+
+    def load(self, verbose: int = 0):
+        """Loads and preprocesses the data. Returns self."""
+        if isinstance(self._data, pandas.DataFrame):
+            if verbose:
+                print(f"[CubeLogs.load] load from dataframe, shape={self._data.shape}")
+            self.data = self._data
+        elif isinstance(self._data, list) and all(isinstance(r, dict) for r in self._data):
+            if verbose:
+                print(f"[CubeLogs.load] load from list of dicts, n={len(self._data)}")
+            self.data = pandas.DataFrame(self._data)
+        elif isinstance(self._data, list) and all(
+            isinstance(r, pandas.DataFrame) for r in self._data
+        ):
+            if verbose:
+                print(f"[CubeLogs.load] load from list of DataFrame, n={len(self._data)}")
+            self.data = pandas.concat(self._data, axis=0)
+        elif isinstance(self._data, list):
+            cubes = []
+            for item in enumerate_csv_files(self._data, verbose=verbose):
+                df = open_dataframe(item)
+                cube = CubeLogs(
+                    df,
+                    time=self._time,
+                    keys=self._keys,
+                    values=self._values,
+                    ignored=self._ignored,
+                    recent=self.recent,
+                )
+                cube.load()
+                cubes.append(cube.data)
+            self.data = pandas.concat(cubes, axis=0)
+        else:
+            raise NotImplementedError(
+                f"Not implemented with the provided data (type={type(self._data)})"
+            )
+
+        assert all(isinstance(c, str) for c in self.data.columns), (
+            f"The class only supports string as column names "
+            f"but found {[c for c in self.data.columns if not isinstance(c, str)]}"
+        )
+        if verbose:
+            print(f"[CubeLogs.load] loaded with shape={self.data.shape}")
+
+        self._initialize_columns()
+        if verbose:
+            print(f"[CubeLogs.load] time={self.time}")
+            print(f"[CubeLogs.load] keys={self.keys}")
+            print(f"[CubeLogs.load] values={self.values}")
+            print(f"[CubeLogs.load] ignored={self.ignored}")
+            print(f"[CubeLogs.load] ignored_values={self.ignored_values}")
+            print(f"[CubeLogs.load] ignored_keys={self.ignored_keys}")
+        assert not (
+            set(self.keys) & set(self.values)
+        ), f"Columns {set(self.keys) & set(self.values)} cannot be keys and values"
+        assert not (
+            set(self.keys) & set(self.ignored)
+        ), f"Columns {set(self.keys) & set(self.ignored)} cannot be keys and ignored"
+        assert not (
+            set(self.values) & set(self.ignored)
+        ), f"Columns {set(self.keys) & set(self.ignored)} cannot be values and ignored"
+        assert (
+            self.time not in self.keys
+            and self.time not in self.values
+            and self.time not in self.ignored
+        ), f"Column {self.time!r} is also a key, a value or ignored"
+        self._columns = [self.time, *self.keys, *self.values, *self.ignored]
+        self.dropped = [c for c in self.data.columns if c not in set(self.columns)]
+        self.data = self.data[self.columns]
+        if verbose:
+            print(f"[CubeLogs.load] dropped={self.dropped}")
+            print(f"[CubeLogs.load] data.shape={self.data.shape}")
+
+        self._preprocess()
+        if self.recent and verbose:
+            print(f"[CubeLogs.load] keep most recent data.shape={self.data.shape}")
+
+        # Let's apply the formulas
+        if self._formulas:
+            cols = set(self.data.columns)
+            for k, f in self._formulas.items():
+                if k in cols:
+                    if verbose:
+                        print(f"[CubeLogs.load] skip formula {k!r}")
+                else:
+                    if verbose:
+                        print(f"[CubeLogs.load] apply formula {k!r}")
+                    self.data[k] = f(self.data)
+        self.values_for_key = {k: set(self.data[k]) for k in self.keys}
+        nans = [
+            c for c in [self.time, *self.keys] if self.data[c].isna().astype(int).sum() > 0
+        ]
+        assert not nans, f"The following keys {nans} have nan values. This is not allowed."
+        if verbose:
+            print(f"[CubeLogs.load] convert column {self.time!r} into date")
+        self.data[self.time] = pandas.to_datetime(self.data[self.time])
+        if verbose:
+            print(f"[CubeLogs.load] done, shape={self.shape}")
+        return self
+
+    @property
+    def shape(self) -> Tuple[int, int]:
+        "Returns the shape."
+        assert hasattr(self, "data"), "Method load was not called"
+        return self.data.shape
+
+    @property
+    def columns(self) -> Sequence[str]:
+        "Returns the columns."
+        assert hasattr(self, "data"), "Method load was not called"
+        return self.data.columns
+
+    def _preprocess(self):
+        last = self.values[0]
+        gr = self.data[[self.time, *self.keys, last]].groupby([self.time, *self.keys]).count()
+        gr = gr[gr[last] > 1]
+        if self.recent:
+            cp = self.data.copy()
+            assert (
+                "__index__" not in cp.columns
+            ), f"'__index__' should not be a column in {cp.columns}"
+            cp["__index__"] = np.arange(cp.shape[0])
+            gr = (
+                cp[[*self.keys, self.time, "__index__"]]
+                .groupby(self.keys, as_index=False)
+                .max()
+            )
+            filtered = pandas.merge(cp, gr, on=[self.time, "__index__", *self.keys])
+            assert filtered.shape[0] <= self.data.shape[0], (
+                f"Keeping the latest row brings more row {filtered.shape} "
+                f"(initial is {self.data.shape})."
+            )
+            self.data = filtered.drop("__index__", axis=1)
+        else:
+            assert gr.shape[0] == 0, f"There are duplicated rows:\n{gr}"
+            gr = self.data[[*self.keys, self.time]].groupby(self.keys).count()
+            gr = gr[gr[self.time] > 1]
+            assert (
+                gr.shape[0] == 0
+            ), f"recent should be true to keep the most recent row:\n{gr}"
+
+    @classmethod
+    def _filter_column(cls, filters, columns, can_be_empty=False):
+        set_cols = set()
+        for f in filters:
+            reg = re.compile(f)
+            cols = [c for c in columns if reg.search(c)]
+            set_cols |= set(cols)
+        assert (
+            can_be_empty or set_cols
+        ), f"Filters {filters} returns an empty set from {columns}"
+        return sorted(set_cols)
+
+    def _initialize_columns(self):
+        self.keys = self._filter_column(self._keys, self.data.columns)
+        self.values = self._filter_column(self._values, self.data.columns)
+        self.ignored = self._filter_column(self._ignored, self.data.columns, True)
+        assert (
+            self._time in self.data.columns
+        ), f"Column {self._time} not found in {self.data.columns}"
+        ignored_keys = set(self.ignored) & set(self.keys)
+        ignored_values = set(self.ignored) & set(self.values)
+        self.keys = [c for c in self.keys if c not in ignored_keys]
+        self.values = [c for c in self.values if c not in ignored_values]
+        self.ignored_keys = sorted(ignored_keys)
+        self.ignored_values = sorted(ignored_values)
+        self.time = self._time
+
+    def __str__(self) -> str:
+        "usual"
+        return str(self.data) if hasattr(self, "data") else str(self._data)
+
+    def view(self, view_def: CubeViewDef) -> pandas.DataFrame:
+        """
+        Returns a dataframe, a pivot view.
+        `key_index` determines the index, the other key columns determines
+        the columns. If `ignore_unique` is True, every columns with a unique value
+        is removed.
+
+        :param view_def: view definition
+        :return: dataframe
+        """
+        key_agg = self._filter_column(view_def.key_agg, self.keys) if view_def.key_agg else []
+        set_key_agg = set(key_agg)
+        assert set_key_agg <= set(
+            self.keys
+        ), f"Non existing keys in key_agg {set_key_agg - set(self.keys)}"
+
+        values = self._filter_column(view_def.values, self.values)
+        assert set(values) <= set(
+            self.values
+        ), f"Non existing columns in values {set(values) - set(self.values)}"
+
+        if key_agg:
+            key_index = [
+                c
+                for c in self._filter_column(view_def.key_index, self.keys)
+                if c not in set_key_agg
+            ]
+            keys_no_agg = [c for c in self.keys if c not in set_key_agg]
+            data = (
+                self.data[[*keys_no_agg, *values]]
+                .groupby(key_index, as_index=False)
+                .agg(*view_def.agg_args, **(view_def.agg_kwargs or {}))
+            )
+        else:
+            key_index = self._filter_column(view_def.key_index, self.keys)
+            data = self.data[[*self.keys, *values]]
+
+        assert set(key_index) <= set(
+            self.keys
+        ), f"Non existing keys in key_index {set(key_index) - set(self.keys)}"
+
+        set_key_columns = {
+            c for c in self.keys if c not in key_index and c not in set(key_agg)
+        }
+        if view_def.ignore_unique:
+            key_index = [k for k in key_index if len(self.values_for_key[k]) > 1]
+            key_columns = [k for k in set_key_columns if len(self.values_for_key[k]) > 1]
+        else:
+            key_columns = sorted(set_key_columns)
+
+        if view_def.order:
+            assert set(view_def.order) <= set_key_columns, (
+                f"Non existing columns from order in key_columns "
+                f"{set(view_def.order) - set_key_columns}"
+            )
+            key_columns = [
+                *view_def.order,
+                *[c for c in key_columns if c not in view_def.order],
+            ]
+        return data.pivot(index=key_index[::-1], columns=key_columns, values=values)
+
+    def describe(self) -> pandas.DataFrame:
+        """Basic description of all variables."""
+        rows = []
+        for name in self.data.columns:
+            values = self.data[name]
+            dtype = values.dtype
+            nonan = values.dropna()
+            obs = dict(
+                name=name,
+                dtype=str(dtype),
+                missing=len(values) - len(nonan),
+            )
+            if len(nonan) > 0:
+                obs.update(
+                    dict(
+                        min=nonan.min(),
+                        max=nonan.max(),
+                        count=len(nonan),
+                    )
+                )
+                if is_numeric_dtype(nonan):
+                    obs.update(
+                        dict(
+                            mean=nonan.mean(),
+                            sum=nonan.sum(),
+                        )
+                    )
+                else:
+                    unique = set(nonan)
+                    obs["n_values"] = len(unique)
+                    if len(unique) < 20:
+                        obs["values"] = ",".join(map(str, sorted(unique)))
+            rows.append(obs)
+        return pandas.DataFrame(rows).set_index("name")
+
+    def to_excel(
+        self,
+        output: str,
+        views: Dict[str, CubeViewDef],
+        main: Optional[str] = "main",
+        raw: Optional[str] = "raw",
+        verbose: int = 0,
+    ):
+        """
+        Creates an excel file with a list of view.
+
+        :param output: output file to create
+        :param views: list of views to append
+        :param main: add a page with statitcs on all variables
+        :param raw: add a page with the raw data
+        :param verbose: verbosity
+        """
+
+        with pandas.ExcelWriter(output, engine="openpyxl") as writer:
+            if main:
+                assert main not in views, f"{main!r} is duplicated in views {sorted(views)}"
+                df = self.describe()
+                if verbose:
+                    print(f"[CubeLogs.to_helper] add sheet {main!r} with shape {df.shape}")
+                df.to_excel(writer, sheet_name=main, freeze_panes=(1, 1))
+                self._apply_excel_style(main, writer, df)
+            if raw:
+                assert main not in views, f"{main!r} is duplicated in views {sorted(views)}"
+                if verbose:
+                    print(f"[CubeLogs.to_helper] add sheet {raw!r} with shape {self.shape}")
+                self.data.to_excel(writer, sheet_name=raw, freeze_panes=(1, 1), index=True)
+                self._apply_excel_style(raw, writer, self.data)
+
+            for name, view in views.items():
+                df = self.view(view)
+                if verbose:
+                    print(
+                        f"[CubeLogs.to_helper] add sheet {name!r} with shape "
+                        f"{df.shape}, index={df.index.names}, columns={df.columns.names}"
+                    )
+                df.to_excel(
+                    writer,
+                    sheet_name=name,
+                    freeze_panes=(df.index.nlevels, df.columns.nlevels),
+                )
+                self._apply_excel_style(name, writer, df)
+        if verbose:
+            print(f"[CubeLogs.to_helper] done with {len(views)} views")
+
+    def _apply_excel_style(self, name: str, writer: pandas.ExcelWriter, df: pandas.DataFrame):
+        from openpyxl.styles import Alignment
+        from openpyxl.utils import get_column_letter
+
+        # from openpyxl.styles import Font, PatternFill, numbers
+
+        left = Alignment(horizontal="left")
+        right = Alignment(horizontal="right")
+        # center = Alignment(horizontal="center")
+        # bold_font = Font(bold=True)
+        # red = Font(color="FF0000")
+        # yellow = PatternFill(start_color="FFFF00", end_color="FFFF00", fill_type="solid")
+        # redf = PatternFill(start_color="FF0000", end_color="FF0000", fill_type="solid")
+
+        sheet = writer.sheets[name]
+        n_rows = df.shape[0] + df.columns.nlevels + df.index.nlevels
+        n_cols = df.shape[1] + df.index.nlevels
+        co: Dict[int, int] = {}
+        sizes: Dict[int, int] = {}
+        cols = set()
+        for i in range(1, n_rows):
+            for j, cell in enumerate(sheet[i]):
+                if j > n_cols:
+                    break
+                cols.add(cell.column)
+                if isinstance(cell.value, float):
+                    co[j] = co.get(j, 0) + 1
+                elif isinstance(cell.value, str):
+                    sizes[cell.column] = max(sizes.get(cell.column, 0), len(cell.value))
+
+        for k, v in sizes.items():
+            c = get_column_letter(k)
+            sheet.column_dimensions[c].width = max(15, v)
+        for k in cols:
+            if k not in sizes:
+                c = get_column_letter(k)
+                sheet.column_dimensions[c].width = 15
+
+        for i in range(1, n_rows):
+            for j, cell in enumerate(sheet[i]):
+                if j > n_cols:
+                    break
+                if isinstance(cell.value, pandas.Timestamp):
+                    cell.alignment = right
+                    dt = cell.value.to_pydatetime()
+                    cell.value = dt
+                    cell.number_format = (
+                        "YYYY-MM-DD"
+                        if (
+                            dt.hour == 0
+                            and dt.minute == 0
+                            and dt.second == 0
+                            and dt.microsecond == 0
+                        )
+                        else "YYYY-MM-DD 00:00:00"
+                    )
+                elif isinstance(cell.value, (float, int)):
+                    cell.alignment = right
+                    x = abs(cell.value)
+                    if int(x) == x:
+                        cell.number_format = "0"
+                    elif x > 5000:
+                        cell.number_format = "# ##0"
+                    elif x >= 500:
+                        cell.number_format = "0.0"
+                    elif x >= 50:
+                        cell.number_format = "0.00"
+                    elif x >= 5:
+                        cell.number_format = "0.000"
+                    elif x > 0.5:
+                        cell.number_format = "0.0000"
+                    elif x > 0.005:
+                        cell.number_format = "0.00000"
+                    else:
+                        cell.number_format = "0.000E+00"
+                else:
+                    cell.alignment = left

onnx_diagnostic/helpers/mini_onnx_builder.py

@@ -393,7 +393,8 @@ def create_onnx_model_from_input_tensors(
     Creates a model proto including all the value as initializers.
     They can be restored by executing the model.
     We assume these inputs are not bigger than 2Gb,
-    the limit of protobuf.
+    the limit of protobuf. Nothing is implemented yet to get around
+    that limit.
 
     :param inputs: anything
     :param switch_low_high: if None, it is equal to ``switch_low_high=sys.byteorder != "big"``
@@ -532,6 +533,8 @@ def create_input_tensors_from_onnx_model(
     :param engine: runtime to use, onnx, the default value, onnxruntime
     :param sep: separator
     :return: restored data
+
+    See example :ref:`l-plot-intermediate-results` for an example.
     """
     if engine == "ExtendedReferenceEvaluator":
         from ..reference import ExtendedReferenceEvaluator