Merge branch 'develop' of ssh://phabricator.mitk.org:2222/source/trix…

…i into develop

Readme.md

@@ -1,7 +1,7 @@
 [![DOI](https://zenodo.org/badge/134823632.svg)](https://zenodo.org/badge/latestdoi/134823632)
 [![PyPI version](https://badge.fury.io/py/trixi.svg)](https://badge.fury.io/py/trixi)
 [![Build Status](https://img.shields.io/travis/MIC-DKFZ/trixi.svg)](https://travis-ci.org/MIC-DKFZ/trixi)
-[![Documentation Status](https://readthedocs.org/projects/trixi/badge/?version=latest)](https://trixi.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/trixi/badge/?version=develop)](https://trixi.readthedocs.io/en/develop/?badge=develop)
 [![Downloads](https://pepy.tech/badge/trixi)](https://pepy.tech/project/trixi)
 [![GitHub](https://img.shields.io/pypi/l/trixi.svg)](https://github.com/MIC-DKFZ/trixi/blob/master/LICENSE)
 <p align="center">
@@ -13,8 +13,9 @@ Finally get some structure into your machine learning experiments.
 
 * [Features](#features)
 * [Installation](#installation)
-* [Documentation](#documentation) ([trixi.rtfd.io](https://trixi.readthedocs.io/en/latest/))
+* [Documentation](#documentation) ([trixi.rtfd.io](https://trixi.readthedocs.io/en/develop/))
 * [Examples](#examples)
+* [How to Cite](#how-to-cite)
 
 # Contribute
 
@@ -151,3 +152,17 @@ Examples can be found here for:
 * [Experiment Infrastructure](https://github.com/MIC-DKFZ/trixi/blob/master/examples/pytorch_experiment.ipynb) (with a
  simple MNIST Experiment example and resuming and comparison of different hyperparameters)
 * [U-Net Example](https://github.com/MIC-DKFZ/basic_unet_example)
+
+# How to Cite
+
+If you use **trixi** in your project, we'd appreciate a citation, for example like this
+
+    @misc{trixi2017,
+      author = {Zimmerer, David and Petersen, Jens and Köhler, Gregor and Wasserthal, Jakob and Adler, Tim and Wirkert, Sebastian and Ross, Tobias},
+      title = {trixi - Training and Retrospective Insight eXperiment Infrastructure},
+      year = {2017},
+      publisher = {GitHub},
+      journal = {GitHub Repository},
+      howpublished = {\url{https://github.com/MIC-DKFZ/trixi}},
+      doi = {10.5281/zenodo.1345136}
+    }

doc/_api/trixi.logger.rst

@@ -121,15 +121,15 @@ tensorboard
     :undoc-members:
     :show-inheritance:
 
-:hidden:`TensorboardXLogger`
+:hidden:`TensorboardLogger`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. automodule:: trixi.logger.tensorboard.tensorboardxlogger
     :members:
     :undoc-members:
     :show-inheritance:
 
-:hidden:`PytorchTensorboardXLogger`
+:hidden:`PytorchTensorboardLogger`
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. automodule:: trixi.logger.tensorboard.pytorchtensorboardxlogger

requirements_full.txt

@@ -1,8 +1,8 @@
 -r requirements.txt
-torch>=1.1.0
+torch>=1.3.0
 torchvision>=0.2.1
 python-telegram-bot>=10.1.0
 umap-learn>=0.3.6
-scikit-learn==0.20.2
+scikit-learn>=0.20.2
 slackclient>=1.3.1
-tb-nightly==1.14.0a20190523
+tensorboard==2.1.1

test/test_pytorchtensorboardxlogger.py

@@ -12,15 +12,15 @@
 from scipy import misc
 
 from trixi.logger.experiment.experimentlogger import ExperimentLogger
-from trixi.logger.tensorboard.pytorchtensorboardxlogger import PytorchTensorboardXLogger
+from trixi.logger.tensorboard.pytorchtensorboardlogger import PytorchTensorboardLogger
 from trixi.util.config import Config
 
 
 class TestPytorchTensorboardXLogger(unittest.TestCase):
 
     def setUp(self):
         self.test_dir = tempfile.gettempdir()
-        self.logger = PytorchTensorboardXLogger(self.test_dir)
+        self.logger = PytorchTensorboardLogger(self.test_dir)
 
     def tearDown(self):
         self.logger.close()

trixi/experiment/pytorchexperiment.py

@@ -17,22 +17,25 @@
 from trixi.experiment.experiment import Experiment
 from trixi.logger import CombinedLogger, PytorchExperimentLogger, PytorchVisdomLogger
 
-from trixi.logger.tensorboard.pytorchtensorboardxlogger import PytorchTensorboardXLogger
+from trixi.logger.tensorboard.pytorchtensorboardlogger import PytorchTensorboardLogger
 from trixi.util import Config, ResultElement, ResultLogDict, SourcePacker, name_and_iter_to_filename
 from trixi.util.config import update_from_sys_argv
 from trixi.util.pytorchutils import set_seed
 from trixi.util.util import is_picklable
 
 logger_lookup_dict = dict(
     visdom=PytorchVisdomLogger,
-    tensorboard=PytorchTensorboardXLogger,
+    tensorboard=PytorchTensorboardLogger,
 )
 
 try:
-    from trixi.logger import TelegramMessageLogger
     from trixi.logger.message.slackmessagelogger import SlackMessageLogger
-
     logger_lookup_dict["slack"] = SlackMessageLogger
+except:
+    pass
+
+try:
+    from trixi.logger import TelegramMessageLogger
     logger_lookup_dict["telegram"] = TelegramMessageLogger
 except:
     pass

trixi/logger/tensorboard/__init__.py

@@ -1,6 +1,6 @@
-from trixi.logger.tensorboard.tensorboardxlogger import TensorboardXLogger
+from trixi.logger.tensorboard.tensorboardlogger import TensorboardLogger
 try:
-    from trixi.logger.tensorboard.pytorchtensorboardxlogger import PytorchTensorboardXLogger
+    from trixi.logger.tensorboard.pytorchtensorboardlogger import PytorchTensorboardLogger
 except ImportError as e:
     import warnings
     warnings.warn(ImportWarning("Could not import Pytorch related modules:\n%s"

trixi/logger/tensorboard/pytorchtensorboardxlogger.py → trixi/logger/tensorboard/pytorchtensorboardlogger.py

@@ -1,8 +1,8 @@
 import torch
-from trixi.logger.tensorboard.tensorboardxlogger import TensorboardXLogger
+from trixi.logger.tensorboard.tensorboardlogger import TensorboardLogger
 
 
-class PytorchTensorboardXLogger(TensorboardXLogger):
+class PytorchTensorboardLogger(TensorboardLogger):
     """Abstract interface for visual logger."""
 
     def process_params(self, f, *args, **kwargs):
@@ -21,7 +21,7 @@ def process_params(self, f, *args, **kwargs):
         return f(self, *args, **kwargs)
 
     def __init__(self, *args, **kwargs):
-        super(PytorchTensorboardXLogger, self).__init__(*args, **kwargs)
+        super(PytorchTensorboardLogger, self).__init__(*args, **kwargs)
 
     def plot_model_structure(self, model, input_size):
         """

trixi/logger/tensorboard/tensorboardxlogger.py → trixi/logger/tensorboard/tensorboardlogger.py

@@ -9,12 +9,12 @@
 from trixi.util.util import np_make_grid
 
 
-class TensorboardXLogger(NumpySeabornPlotLogger):
-    """Logger that uses tensorboardX to log to Tensorboard."""
+class TensorboardLogger(NumpySeabornPlotLogger):
+    """Logger that uses tensorboard to log to Tensorboard."""
 
     def __init__(self, target_dir, *args, **kwargs):
 
-        super(TensorboardXLogger, self).__init__(*args, **kwargs)
+        super(TensorboardLogger, self).__init__(*args, **kwargs)
 
         os.makedirs(target_dir, exist_ok=True)
 
@@ -280,5 +280,21 @@ def show_pr_curve(self, tensor, labels, name="pr-curve", counter=None, *args, **
 
         self.writer.add_pr_curve(tag=name, labels=labels, predictions=tensor, global_step=self.val_dict["{}-pr-curve".format(name)])
 
+    def show_hparams(self, hparam_dict=None, metric_dict=None, counter=None, *args, **kwargs):
+        """
+
+        Args:
+            hparam_dict: Each key-value pair in the dictionary is the name of the hyper parameter and it’s corresponding value.
+            metric_dict: Each key-value pair in the dictionary is the name of the metric and it’s corresponding value.
+             Note that the key used here should be unique in the tensorboard record. Otherwise the value you added by
+             show_value will be displayed in the hparam plugin. In most cases, this is unwanted.
+        """
+        if counter is not None:
+            self.val_dict["{}-hparams"] = counter
+        else:
+            self.val_dict["{}-hparams"] += 1
+
+        self.writer.add_hparams(hparam_dict=hparam_dict, metric_dict=metric_dict)
+
     def close(self):
         self.writer.close()

trixi/util/pytorchexperimentstub.py

@@ -8,12 +8,12 @@
 
 from trixi.logger import PytorchExperimentLogger, PytorchVisdomLogger, TelegramMessageLogger
 from trixi.logger.message.slackmessagelogger import SlackMessageLogger
-from trixi.logger.tensorboard import PytorchTensorboardXLogger
+from trixi.logger.tensorboard import PytorchTensorboardLogger
 from trixi.util import ResultElement, ResultLogDict, Config
 
 logger_lookup_dict = dict(
     visdom=PytorchVisdomLogger,
-    tensorboard=PytorchTensorboardXLogger,
+    tensorboard=PytorchTensorboardLogger,
     telegram=TelegramMessageLogger,
     slack=SlackMessageLogger,
 )