wandb 0.19.1rc1__py3-none-musllinux_1_2_aarch64.whl

wandb/integration/sklearn/utils.py

@@ -0,0 +1,183 @@
+"""Shared utilities for the modules in wandb.sklearn."""
+
+from collections.abc import Iterable, Sequence
+
+import numpy as np
+import pandas as pd
+import scipy
+import sklearn
+
+import wandb
+
+chart_limit = 1000
+
+
+def check_against_limit(count, chart, limit=None):
+    if limit is None:
+        limit = chart_limit
+    if count > limit:
+        warn_chart_limit(limit, chart)
+        return True
+    else:
+        return False
+
+
+def warn_chart_limit(limit, chart):
+    warning = f"using only the first {limit} datapoints to create chart {chart}"
+    wandb.termwarn(warning)
+
+
+def encode_labels(df):
+    le = sklearn.preprocessing.LabelEncoder()
+    # apply le on categorical feature columns
+    categorical_cols = df.select_dtypes(
+        exclude=["int", "float", "float64", "float32", "int32", "int64"]
+    ).columns
+    df[categorical_cols] = df[categorical_cols].apply(lambda col: le.fit_transform(col))
+
+
+def test_types(**kwargs):
+    test_passed = True
+    for k, v in kwargs.items():
+        # check for incorrect types
+        if (
+            (k == "X")
+            or (k == "X_test")
+            or (k == "y")
+            or (k == "y_test")
+            or (k == "y_true")
+            or (k == "y_probas")
+        ):
+            # FIXME: do this individually
+            if not isinstance(
+                v,
+                (
+                    Sequence,
+                    Iterable,
+                    np.ndarray,
+                    np.generic,
+                    pd.DataFrame,
+                    pd.Series,
+                    list,
+                ),
+            ):
+                wandb.termerror(f"{k} is not an array. Please try again.")
+                test_passed = False
+        # check for classifier types
+        if k == "model":
+            if (not sklearn.base.is_classifier(v)) and (
+                not sklearn.base.is_regressor(v)
+            ):
+                wandb.termerror(
+                    f"{k} is not a classifier or regressor. Please try again."
+                )
+                test_passed = False
+        elif k == "clf" or k == "binary_clf":
+            if not (sklearn.base.is_classifier(v)):
+                wandb.termerror(f"{k} is not a classifier. Please try again.")
+                test_passed = False
+        elif k == "regressor":
+            if not sklearn.base.is_regressor(v):
+                wandb.termerror(f"{k} is not a regressor. Please try again.")
+                test_passed = False
+        elif k == "clusterer":
+            if not (getattr(v, "_estimator_type", None) == "clusterer"):
+                wandb.termerror(f"{k} is not a clusterer. Please try again.")
+                test_passed = False
+    return test_passed
+
+
+def test_fitted(model):
+    try:
+        model.predict(np.zeros((7, 3)))
+    except sklearn.exceptions.NotFittedError:
+        wandb.termerror("Please fit the model before passing it in.")
+        return False
+    except AttributeError:
+        # Some clustering models (LDA, PCA, Agglomerative) don't implement ``predict``
+        try:
+            sklearn.utils.validation.check_is_fitted(
+                model,
+                [
+                    "coef_",
+                    "estimator_",
+                    "labels_",
+                    "n_clusters_",
+                    "children_",
+                    "components_",
+                    "n_components_",
+                    "n_iter_",
+                    "n_batch_iter_",
+                    "explained_variance_",
+                    "singular_values_",
+                    "mean_",
+                ],
+                all_or_any=any,
+            )
+            return True
+        except sklearn.exceptions.NotFittedError:
+            wandb.termerror("Please fit the model before passing it in.")
+            return False
+    except Exception:
+        # Assume it's fitted, since ``NotFittedError`` wasn't raised
+        return True
+
+
+# Test Asummptions for plotting parameters and datasets
+def test_missing(**kwargs):
+    test_passed = True
+    for k, v in kwargs.items():
+        # Missing/empty params/datapoint arrays
+        if v is None:
+            wandb.termerror(f"{k} is None. Please try again.")
+            test_passed = False
+        if (k == "X") or (k == "X_test"):
+            if isinstance(v, scipy.sparse.csr.csr_matrix):
+                v = v.toarray()
+            elif isinstance(v, (pd.DataFrame, pd.Series)):
+                v = v.to_numpy()
+            elif isinstance(v, list):
+                v = np.asarray(v)
+
+            # Warn the user about missing values
+            missing = 0
+            missing = np.count_nonzero(pd.isnull(v))
+            if missing > 0:
+                wandb.termwarn(f"{k} contains {missing} missing values. ")
+                test_passed = False
+            # Ensure the dataset contains only integers
+            non_nums = 0
+            if v.ndim == 1:
+                non_nums = sum(
+                    1
+                    for val in v
+                    if (
+                        not isinstance(val, (int, float, complex))
+                        and not isinstance(val, np.number)
+                    )
+                )
+            else:
+                non_nums = sum(
+                    1
+                    for sl in v
+                    for val in sl
+                    if (
+                        not isinstance(val, (int, float, complex))
+                        and not isinstance(val, np.number)
+                    )
+                )
+            if non_nums > 0:
+                wandb.termerror(
+                    f"{k} contains values that are not numbers. Please vectorize, label encode or one hot encode {k} "
+                    "and call the plotting function again."
+                )
+                test_passed = False
+    return test_passed
+
+
+def round_3(n):
+    return round(n, 3)
+
+
+def round_2(n):
+    return round(n, 2)

wandb/integration/tensorboard/__init__.py

@@ -0,0 +1,10 @@
+"""wandb integration tensorboard module."""
+
+from .log import _log, log, reset_state, tf_summary_to_dict  # noqa: F401
+from .monkeypatch import patch, unpatch
+
+__all__ = [
+    "patch",
+    "unpatch",
+    "log",
+]

wandb/integration/tensorboard/log.py

@@ -0,0 +1,354 @@
+import io
+import re
+import time
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Union
+
+import wandb
+import wandb.util
+from wandb.sdk.lib import telemetry
+
+if TYPE_CHECKING:
+    import numpy as np
+
+    from wandb.sdk.internal.tb_watcher import TBHistory
+
+# We have at least the default namestep and a global step to track
+# TODO: reset this structure on wandb.finish
+STEPS: Dict[str, Dict[str, Any]] = {
+    "": {"step": 0},
+    "global": {"step": 0, "last_log": None},
+}
+# TODO(cling): Set these when tensorboard behavior is configured.
+# We support rate limited logging by setting this to number of seconds,
+# can be a floating point.
+RATE_LIMIT_SECONDS: Optional[Union[float, int]] = None
+IGNORE_KINDS = ["graphs"]
+tensor_util = wandb.util.get_module("tensorboard.util.tensor_util")
+
+
+# prefer tensorboard, fallback to protobuf in tensorflow when tboard isn't available
+pb = wandb.util.get_module(
+    "tensorboard.compat.proto.summary_pb2"
+) or wandb.util.get_module("tensorflow.core.framework.summary_pb2")
+
+Summary = pb.Summary if pb else None
+
+
+def make_ndarray(tensor: Any) -> Optional["np.ndarray"]:
+    if tensor_util:
+        res = tensor_util.make_ndarray(tensor)
+        # Tensorboard can log generic objects, and we don't want to save them
+        if res.dtype == "object":
+            return None
+        else:
+            return res  # type: ignore
+    else:
+        wandb.termwarn(
+            "Can't convert tensor summary, upgrade tensorboard with `pip"
+            " install tensorboard --upgrade`"
+        )
+        return None
+
+
+def namespaced_tag(tag: str, namespace: str = "") -> str:
+    if not namespace:
+        return tag
+    else:
+        return namespace + "/" + tag
+
+
+def history_image_key(key: str, namespace: str = "") -> str:
+    """Convert invalid filesystem characters to _ for use in History keys.
+
+    Unfortunately this means currently certain image keys will collide silently. We
+    implement this mapping up here in the TensorFlow stuff rather than in the History
+    stuff so that we don't have to store a mapping anywhere from the original keys to
+    the safe ones.
+    """
+    return namespaced_tag(re.sub(r"[/\\]", "_", key), namespace)
+
+
+def tf_summary_to_dict(  # noqa: C901
+    tf_summary_str_or_pb: Any, namespace: str = ""
+) -> Optional[Dict[str, Any]]:
+    """Convert a Tensorboard Summary to a dictionary.
+
+    Accepts a tensorflow.summary.Summary, one encoded as a string,
+    or a list of such encoded as strings.
+    """
+    values = {}
+    if hasattr(tf_summary_str_or_pb, "summary"):
+        summary_pb = tf_summary_str_or_pb.summary
+        values[namespaced_tag("global_step", namespace)] = tf_summary_str_or_pb.step
+        values["_timestamp"] = tf_summary_str_or_pb.wall_time
+    elif isinstance(tf_summary_str_or_pb, (str, bytes, bytearray)):
+        summary_pb = Summary()
+        summary_pb.ParseFromString(tf_summary_str_or_pb)
+    elif hasattr(tf_summary_str_or_pb, "__iter__"):
+        summary_pb = [Summary() for _ in range(len(tf_summary_str_or_pb))]
+        for i, summary in enumerate(tf_summary_str_or_pb):
+            summary_pb[i].ParseFromString(summary)
+            if i > 0:
+                summary_pb[0].MergeFrom(summary_pb[i])
+        summary_pb = summary_pb[0]
+    else:
+        summary_pb = tf_summary_str_or_pb
+
+    if not hasattr(summary_pb, "value") or len(summary_pb.value) == 0:
+        # Ignore these, caller is responsible for handling None
+        return None
+
+    def encode_images(_img_strs: List[bytes], _value: Any) -> None:
+        try:
+            from PIL import Image
+        except ImportError:
+            wandb.termwarn(
+                "Install pillow if you are logging images with Tensorboard. "
+                "To install, run `pip install pillow`.",
+                repeat=False,
+            )
+            return None
+
+        if len(_img_strs) == 0:
+            return None
+
+        images: List[Union[wandb.Video, wandb.Image]] = []
+        for _img_str in _img_strs:
+            # Supports gifs from TensorboardX
+            if _img_str.startswith(b"GIF"):
+                images.append(wandb.Video(io.BytesIO(_img_str), format="gif"))
+            else:
+                images.append(wandb.Image(Image.open(io.BytesIO(_img_str))))
+        tag_idx = _value.tag.rsplit("/", 1)
+        if len(tag_idx) > 1 and tag_idx[1].isdigit():
+            tag, idx = tag_idx
+            values.setdefault(history_image_key(tag, namespace), []).extend(images)
+        else:
+            values[history_image_key(_value.tag, namespace)] = images
+
+        return None
+
+    for value in summary_pb.value:
+        kind = value.WhichOneof("value")
+        if kind in IGNORE_KINDS:
+            continue
+        if kind == "simple_value":
+            values[namespaced_tag(value.tag, namespace)] = value.simple_value
+        elif kind == "tensor":
+            plugin_name = value.metadata.plugin_data.plugin_name
+            if plugin_name == "scalars" or plugin_name == "":
+                values[namespaced_tag(value.tag, namespace)] = make_ndarray(
+                    value.tensor
+                )
+            elif plugin_name == "images":
+                img_strs = value.tensor.string_val[2:]  # First two items are dims.
+                encode_images(img_strs, value)
+            elif plugin_name == "histograms":
+                # https://github.com/tensorflow/tensorboard/blob/master/tensorboard/plugins/histogram/summary_v2.py#L15-L26
+                ndarray = make_ndarray(value.tensor)
+                if ndarray is None:
+                    continue
+                shape = ndarray.shape
+                counts = []
+                bins = []
+                if shape[0] > 1:
+                    bins.append(ndarray[0][0])  # Add the left most edge
+                    for v in ndarray:
+                        counts.append(v[2])
+                        bins.append(v[1])  # Add the right most edges
+                elif shape[0] == 1:
+                    counts = [ndarray[0][2]]
+                    bins = ndarray[0][:2]
+                if len(counts) > 0:
+                    try:
+                        # TODO: we should just re-bin if there are too many buckets
+                        values[namespaced_tag(value.tag, namespace)] = wandb.Histogram(
+                            np_histogram=(counts, bins)  # type: ignore
+                        )
+                    except ValueError:
+                        wandb.termwarn(
+                            'Not logging key "{}". '
+                            "Histograms must have fewer than {} bins".format(
+                                namespaced_tag(value.tag, namespace),
+                                wandb.Histogram.MAX_LENGTH,
+                            ),
+                            repeat=False,
+                        )
+            elif plugin_name == "pr_curves":
+                pr_curve_data = make_ndarray(value.tensor)
+                if pr_curve_data is None:
+                    continue
+                precision = pr_curve_data[-2, :].tolist()
+                recall = pr_curve_data[-1, :].tolist()
+                # TODO: (kdg) implement spec for showing additional info in tool tips
+                # true_pos = pr_curve_data[1,:]
+                # false_pos = pr_curve_data[2,:]
+                # true_neg = pr_curve_data[1,:]
+                # false_neg = pr_curve_data[1,:]
+                # threshold = [1.0 / n for n in range(len(true_pos), 0, -1)]
+                # min of each in case tensorboard ever changes their pr_curve
+                # to allow for different length outputs
+                data = []
+                for i in range(min(len(precision), len(recall))):
+                    # drop additional threshold values if they exist
+                    if precision[i] != 0 or recall[i] != 0:
+                        data.append((recall[i], precision[i]))
+                # sort data so custom chart looks the same as tb generated pr curve
+                # ascending recall, descending precision for the same recall values
+                data = sorted(data, key=lambda x: (x[0], -x[1]))
+                data_table = wandb.Table(data=data, columns=["recall", "precision"])
+                name = namespaced_tag(value.tag, namespace)
+
+                values[name] = wandb.plot_table(
+                    "wandb/line/v0",
+                    data_table,
+                    {"x": "recall", "y": "precision"},
+                    {"title": f"{name} Precision v. Recall"},
+                )
+        elif kind == "image":
+            img_str = value.image.encoded_image_string
+            encode_images([img_str], value)
+        # Coming soon...
+        # elif kind == "audio":
+        #     audio = wandb.Audio(
+        #         six.BytesIO(value.audio.encoded_audio_string),
+        #         sample_rate=value.audio.sample_rate,
+        #         content_type=value.audio.content_type,
+        #     )
+        elif kind == "histo":
+            tag = namespaced_tag(value.tag, namespace)
+            if len(value.histo.bucket_limit) >= 3:
+                first = (
+                    value.histo.bucket_limit[0]
+                    + value.histo.bucket_limit[0]
+                    - value.histo.bucket_limit[1]
+                )
+                last = (
+                    value.histo.bucket_limit[-2]
+                    + value.histo.bucket_limit[-2]
+                    - value.histo.bucket_limit[-3]
+                )
+                np_histogram = (
+                    list(value.histo.bucket),
+                    [first] + value.histo.bucket_limit[:-1] + [last],
+                )
+                try:
+                    # TODO: we should just re-bin if there are too many buckets
+                    values[tag] = wandb.Histogram(np_histogram=np_histogram)  # type: ignore
+                except ValueError:
+                    wandb.termwarn(
+                        f"Not logging key {tag!r}. "
+                        f"Histograms must have fewer than {wandb.Histogram.MAX_LENGTH} bins",
+                        repeat=False,
+                    )
+            else:
+                # TODO: is there a case where we can render this?
+                wandb.termwarn(
+                    f"Not logging key {tag!r}. Found a histogram with only 2 bins.",
+                    repeat=False,
+                )
+        # TODO(jhr): figure out how to share this between userspace and internal process or dont
+        # elif value.tag == "_hparams_/session_start_info":
+        #     if wandb.util.get_module("tensorboard.plugins.hparams"):
+        #         from tensorboard.plugins.hparams import plugin_data_pb2
+        #
+        #         plugin_data = plugin_data_pb2.HParamsPluginData()        #
+        #         plugin_data.ParseFromString(value.metadata.plugin_data.content)
+        #         for key, param in six.iteritems(plugin_data.session_start_info.hparams):
+        #             if not wandb.run.config.get(key):
+        #                 wandb.run.config[key] = (
+        #                     param.number_value or param.string_value or param.bool_value
+        #                 )
+        #     else:
+        #         wandb.termerror(
+        #             "Received hparams tf.summary, but could not import "
+        #             "the hparams plugin from tensorboard"
+        #         )
+    return values
+
+
+def reset_state() -> None:
+    """Internal method for resetting state, called by wandb.finish()."""
+    global STEPS
+    STEPS = {"": {"step": 0}, "global": {"step": 0, "last_log": None}}
+
+
+def _log(
+    tf_summary_str_or_pb: Any,
+    history: Optional["TBHistory"] = None,
+    step: int = 0,
+    namespace: str = "",
+    **kwargs: Any,
+) -> None:
+    """Logs a tfsummary to wandb.
+
+    Can accept a tf summary string or parsed event.  Will use wandb.run.history unless a
+    history object is passed.  Can optionally namespace events.  Results are committed
+    when step increases for this namespace.
+
+    NOTE: This assumes that events being passed in are in chronological order
+    """
+    global STEPS
+    global RATE_LIMIT_SECONDS
+    # To handle multiple global_steps, we keep track of them here instead
+    # of the global log
+    last_step = STEPS.get(namespace, {"step": 0})
+
+    # Commit our existing data if this namespace increased its step
+    commit = False
+    if last_step["step"] < step:
+        commit = True
+
+    log_dict = tf_summary_to_dict(tf_summary_str_or_pb, namespace)
+    if log_dict is None:
+        # not an event, just return
+        return
+
+    # Pass timestamp to history for loading historic data
+    timestamp = log_dict.get("_timestamp", time.time())
+    # Store our initial timestamp
+    if STEPS["global"]["last_log"] is None:
+        STEPS["global"]["last_log"] = timestamp
+    # Rollup events that share the same step across namespaces
+    if commit and step == STEPS["global"]["step"]:
+        commit = False
+    # Always add the biggest global_step key for non-default namespaces
+    if step > STEPS["global"]["step"]:
+        STEPS["global"]["step"] = step
+    if namespace != "":
+        log_dict["global_step"] = STEPS["global"]["step"]
+
+    # Keep internal step counter
+    STEPS[namespace] = {"step": step}
+
+    if commit:
+        # Only commit our data if we're below the rate limit or don't have one
+        if (
+            RATE_LIMIT_SECONDS is None
+            or timestamp - STEPS["global"]["last_log"] >= RATE_LIMIT_SECONDS
+        ):
+            if history is None:
+                if wandb.run is not None:
+                    wandb.run._log({})
+            else:
+                history.add({})
+
+        STEPS["global"]["last_log"] = timestamp
+
+    if history is None:
+        if wandb.run is not None:
+            wandb.run._log(log_dict, commit=False)
+    else:
+        history._row_update(log_dict)
+
+
+def log(tf_summary_str_or_pb: Any, step: int = 0, namespace: str = "") -> None:
+    if wandb.run is None:
+        raise wandb.Error(
+            "You must call `wandb.init()` before calling `wandb.tensorflow.log`"
+        )
+
+    with telemetry.context() as tel:
+        tel.feature.tensorboard_log = True
+
+    _log(tf_summary_str_or_pb, namespace=namespace, step=step)