- Added first evaluation script

- Fixed bug when loading multiple files

setup.py

@@ -7,6 +7,8 @@ entry_points = {
     "console_scripts": [
         "robofish-io-validate=robofish.io.app:validate",
         "robofish-io-print=robofish.io.app:print",
+        # TODO: This should be called robofish-evaluate which is not possible because of the package name (guess) ask moritzs
+        "robofish-io-evaluate=robofish.evaluate.app:evaluate",
     ]
 }
 setup(

src/robofish/evaluate/__init__.py

+import sys
+import logging
+
+import robofish.io
+
+from robofish.evaluate.evaluate import *
+import robofish.evaluate.app
+
+# TODO: REMOVE
+# logging.getLogger().setLevel(logging.INFO)
+
+assert (3, 7) <= sys.version_info < (4, 0), "Unsupported Python version"

src/robofish/evaluate/app.py

+# -*- coding: utf-8 -*-
+
+# -----------------------------------------------------------
+# Functions available to be used in the commandline to evaluate robofish.io files
+#
+# Dec 2020 Andreas Gerken, Berlin, Germany
+# Released under GNU 3.0 License
+# email andi.gerken@gmail.com
+# -----------------------------------------------------------
+
+import robofish.evaluate
+
+import argparse
+
+
+def evaluate(args=None):
+    """This function can be used to print hdf5 files from the command line
+
+    Returns:
+        A human readable print of a given hdf5 file.
+    """
+    parser = argparse.ArgumentParser(description="TODO")
+
+    parser.add_argument("analysis_type", type=str, choices=["speed"])
+    parser.add_argument(
+        "paths",
+        type=str,
+        nargs="+",
+        help="The paths to io/hdf5 files. Multiple paths can be given which will be shown in different colors",
+    )
+
+    if args is None:
+        args = parser.parse_args()
+
+    if args.analysis_type == "speed":
+        robofish.evaluate.evaluate.evaluate_speed(args.paths)

src/robofish/evaluate/evaluate.py

+import robofish.evaluate
+import robofish.io
+import matplotlib.pyplot as plt
+import seaborn as sns
+
+import numpy as np
+
+
+def evaluate_speed(paths):
+
+    files_per_path = [robofish.io.read_multiple_files(p) for p in paths]
+    speeds = []
+    for files in files_per_path:
+        path_speeds = []
+        for p, file in files.items():
+            poses = file.get_poses_array()
+            for e_poses in poses:
+                e_speeds = np.linalg.norm(np.diff(e_poses[:, :2], axis=0), axis=1)
+                path_speeds.extend(e_speeds)
+
+        speeds.append(path_speeds)
+
+    plt.hist(speeds, bins=20, label=paths, density=True, range=[0, 1])
+    # sns.displot(speeds, label=paths, multiple="layer", kind="kde")
+    plt.title("Agent speeds")
+    plt.xlabel("Speed (cm/timestep)")
+    plt.ylabel("Frequency (logscale)")
+    plt.ticklabel_format(useOffset=False)
+    # plt.xscale("log", nonpositive="clip")
+    plt.legend()
+    plt.tight_layout()
+    plt.show()

src/robofish/io/__init__.py

 # SPDX-License-Identifier: LGPL-3.0-or-later
 
 import sys
+import logging
+
+# TODO: REMOVE
+logging.getLogger().setLevel(logging.INFO)
+
 from robofish.io.file import File
 from robofish.io.validation import *
 from robofish.io.io import *

src/robofish/io/file.py

@@ -223,8 +223,11 @@ class File(h5py.File):
             names = self["entities"].keys()
 
         n = len(names)
-        timesteps = max(
-            [self["entities"][e_name]["poses"].shape[0] for e_name in names]
+
+        timesteps = (
+            0
+            if n == 0
+            else max([self["entities"][e_name]["poses"].shape[0] for e_name in names])
         )
 
         # Initialize poses output array

src/robofish/io/io.py

@@ -4,6 +4,17 @@ from typing import Union, Iterable
 from pathlib import Path
 import logging
 
+import numpy as np
+
+# Optional pandas series support
+list_types = (list, np.ndarray)
+try:
+    import pandas
+
+    list_types += (pandas.core.series.Series,)
+except ImportError:
+    pass
+
 
 def now_iso8061():
     return datetime.datetime.now(datetime.timezone.utc).isoformat(
@@ -29,16 +40,16 @@ def read_multiple_files(
 
     logging.info(f"Reading files from path {paths}")
 
-    try:
-        iter(paths)
-    except TypeError:
+    if not isinstance(paths, list_types):
         paths = [paths]
+
     paths = [Path(p) for p in paths]
 
     sf_dict = {}
 
     for path in paths:
         if path.is_dir():
+            logging.info("found dir %s" % path)
             # Find all hdf5 files in folder
             files = []
             for ext in ("hdf", "hdf5", "h5", "he5"):
@@ -51,7 +62,8 @@ def read_multiple_files(
                 sf_dict.update(
                     {file: robofish.io.File(path=file, strict_validate=strict_validate)}
                 )
-        elif path is not None:
+        elif path is not None and path.exists():
+            logging.info("found file %s" % path)
             sf_dict[path] = robofish.io.File(path=path, strict_validate=strict_validate)
 
     return sf_dict