diff --git a/.github/workflows/cmake-macos.yml b/.github/workflows/cmake-macos.yml
index fccabf499fd9f9803590e8dbc667c58f3fc0d7f9..5efc97284d6f00c8ad86912dd45780f1716c5865 100644
--- a/.github/workflows/cmake-macos.yml
+++ b/.github/workflows/cmake-macos.yml
@@ -71,5 +71,5 @@ jobs:
echo "::group::TestFunctions"
conda install -y unzip
cd $GITHUB_WORKSPACE/Application/Tests
- ./run_macos.bash
+ ./run_unix.bash
echo "::endgroup::"
diff --git a/.github/workflows/cmake-ubuntu.yml b/.github/workflows/cmake-ubuntu.yml
index 0e406ffdc3fa491332c2de69251139ca9e3aa9a2..d68196eedf588bd24c4b75d71d470743e1069a25 100644
--- a/.github/workflows/cmake-ubuntu.yml
+++ b/.github/workflows/cmake-ubuntu.yml
@@ -57,11 +57,11 @@ jobs:
cat meta.yaml
echo "::endgroup::"
echo "::group::Build"
- conda build . -c main -c conda-forge
+ conda build .
echo "::endgroup::"
echo "::group::Test"
echo $CONDA_PREFIX
- conda create -y -n test -c main -c conda-forge -c $CONDA_PREFIX/conda-bld/ trex
+ conda create -y -n test -c $CONDA_PREFIX/conda-bld/ trex
conda activate test
pvinfo -opencv_ffmpeg_support
pvinfo -opencv_opencl_support
@@ -69,5 +69,5 @@ jobs:
echo "::group::TestFunctions"
conda install -y unzip
cd $GITHUB_WORKSPACE/Application/Tests
- ./run_ubuntu.bash
+ ./run_unix.bash
echo "::endgroup::"
diff --git a/Application/Tests/run_macos.bash b/Application/Tests/run_macos.bash
deleted file mode 100755
index 3e79526919f68bb28ec47705ebf8aae10f643099..0000000000000000000000000000000000000000
--- a/Application/Tests/run_macos.bash
+++ /dev/null
@@ -1,27 +0,0 @@
-PWD=$(pwd)/../../videos
-
-if ! tgrabs -d "${PWD}" -i "${PWD}/test_frames/frame_%3d.jpg" \
- -o test -threshold 9 -average_samples 100 -averaging_method mode -meta_real_width 2304 -exec "${PWD}/test.settings" \
- -enable_live_tracking -auto_no_results -nowindow -output_format csv; then
- echo "TGrabs could not be executed."
- exit 1
-fi
-
-exit_code=0
-
-for f in `ls ${PWD}/data/test_fish*.csv`; do
- f=$(basename $f .csv)
-
- echo "Checking $f ..."
- if ! git --no-pager diff --word-diff --no-index -- ${PWD}/data/${f}.csv ${PWD}/compare_data/raw/${f}.csv; then
- echo "files $f differ from baseline"
- exit_code=1
- fi
-done
-
-rm -rf ${PWD}/data
-
-exit ${exit_code}
-
-#trex -d "${PWD}" -i test -s "${PWD}/test.settings" -p corrected -auto_apply -auto_quit -auto_no_results -nowindow
-#rm -rf ${PWD}/corrected/data
\ No newline at end of file
diff --git a/Application/Tests/run_ubuntu.bash b/Application/Tests/run_ubuntu.bash
deleted file mode 100755
index 5a3fc8df5a10772b21261b2a94344807a3ecefe0..0000000000000000000000000000000000000000
--- a/Application/Tests/run_ubuntu.bash
+++ /dev/null
@@ -1,23 +0,0 @@
-PWD=$(pwd)/../../videos
-
-if ! tgrabs -d "${PWD}" -i "${PWD}/test_frames/frame_%3d.jpg" \
- -o test -threshold 9 -average_samples 100 -averaging_method mode -meta_real_width 2304 -exec "${PWD}/test.settings" \
- -enable_live_tracking -auto_no_results -nowindow -output_format csv; then
- echo "TGrabs could not be executed."
- exit 1
-fi
-
-for f in `ls ${PWD}/data/test_fish*.csv`; do
- f=$(basename $f .csv)
-
- echo "Checking $f ..."
- if ! git --no-pager diff --word-diff --no-index -- ${PWD}/data/${f}.csv ${PWD}/compare_data/raw/${f}.csv; then
- echo "files $f differ from baseline"
- exit 1
- fi
-done
-
-rm -rf ${PWD}/data
-
-#trex -d "${PWD}" -i test -s "${PWD}/test.settings" -p corrected -auto_apply -auto_quit -auto_no_results -nowindow
-#rm -rf ${PWD}/corrected/data
\ No newline at end of file
diff --git a/Application/Tests/run_unix.bash b/Application/Tests/run_unix.bash
new file mode 100755
index 0000000000000000000000000000000000000000..7c048717201383233b8a7be043816bd000155673
--- /dev/null
+++ b/Application/Tests/run_unix.bash
@@ -0,0 +1,71 @@
+#!/bin/bash
+
+PWD=$(pwd)/../../videos
+
+CMD="tgrabs -d "${PWD}" -i \"${PWD}/test_frames/frame_%3d.jpg\" -o test -threshold 9 -average_samples 100
+ -averaging_method mode -meta_real_width 2304 -exec \"${PWD}/test.settings\"
+ -enable_live_tracking -auto_no_results -output_format csv -nowindow"
+echo "Running TGrabs... ${CMD}"
+if ! { ${CMD} 2>&1; } > "${PWD}/tgrabs.log"; then
+ cat "${PWD}/tgrabs.log"
+ echo "TGrabs could not be executed."
+ exit_code=1
+else
+ echo " Scanning files..."
+ FILES=$(ls ${PWD}/data/test_fish*.csv)
+
+ if [ -z "${FILES}" ]; then
+ echo "[ERROR] No files found."
+ exit_code=1
+ else
+ for f in ${FILES}; do
+ f=$(basename $f .csv)
+
+ echo -e -n "\tChecking $f ..."
+ if ! git --no-pager diff --word-diff --no-index -- ${PWD}/data/${f}.csv ${PWD}/compare_data/raw/${f}.csv; then
+ echo "FAIL"
+ echo "[ERROR] file $f differs from baseline"
+ exit_code=1
+ else
+ echo 'OK'
+ fi
+ done
+ fi
+fi
+
+rm -rf ${PWD}/data
+echo ""
+CMD="trex -d \"${PWD}\" -i test -s \"${PWD}/test.settings\" -p corrected -auto_quit -auto_no_results -output_format csv -nowindow"
+
+echo "Running TRex... ${CMD}"
+
+if ! { ${CMD} 2>&1; } > "${PWD}/trex.log"; then
+ cat "${PWD}/trex.log"
+ echo "TRex could not be executed."
+ exit_code=1
+else
+ echo " Scanning files..."
+ FILES=$(ls ${PWD}/corrected/data/test_fish*.csv)
+
+ if [ -z "${FILES}" ]; then
+ echo "[ERROR] No files found."
+ exit_code=1
+ else
+ for f in ${FILES}; do
+ f=$(basename $f .csv)
+
+ echo -e -n "\tChecking $f ..."
+ if ! git --no-pager diff --word-diff --no-index -- ${PWD}/corrected/data/${f}.csv ${PWD}/compare_data/raw/${f}.csv; then
+ echo "FAIL"
+ echo "[ERROR] corrected file $f differs from baseline"
+ exit_code=1
+ else
+ echo 'OK'
+ fi
+ done
+ fi
+fi
+
+rm -rf ${PWD}/corrected/data
+
+exit ${exit_code}
diff --git a/Application/learn_static.py b/Application/learn_static.py
index be4e2f1600b0e57a3bd6af86dcd3d62573d4891e..d873ec03bd3b551e8b1a4e995cd724f830dd6b7c 100644
--- a/Application/learn_static.py
+++ b/Application/learn_static.py
@@ -228,7 +228,7 @@ class ValidationCallback(keras.callbacks.Callback):
if len(images) == 0:
continue
- Y = self.model.predict(images)
+ Y = self.model.predict(tf.cast(images, float))
predictions.append(Y)
distance = np.abs(Y - zeros).sum(axis=1)
@@ -467,7 +467,7 @@ def predict():
print("error with the shape")
indexes = np.array(np.arange(len(train_X)), dtype=np.float32)
- output = np.array(model.predict(train_X), dtype=np.float32)
+ output = np.array(model.predict(tf.cast(train_X, float)), dtype=np.float32)
receive(output, indexes)
@@ -594,18 +594,21 @@ def start_learning():
callback = ValidationCallback(model, classes, X_test, Y_test, epochs, filename, output_prefix+"_"+str(accumulation_step), output_path, best_accuracy_worst_class, estimate_uniqueness, settings)
- validation_data = (tf.cast(X_test, float), Y_test)
+ validation_data = None
#validation_data = tf.data.Dataset.from_tensor_slices((tf.cast(X_test, float), Y_test))#.batch(batch_size)
if len(X_test) == 0:
validation_data = None
+ else:
+ validation_data = tf.data.Dataset.from_tensor_slices((tf.cast(X_test, float), Y_test)).batch(batch_size)
- dataset = tf.data.Dataset.from_generator(lambda: datagen.flow(tf.cast(X_train, float), Y_train, batch_size=batch_size),
+ dataset = tf.data.Dataset.from_generator(lambda: datagen.flow(tf.cast(X_train, float), tf.cast(Y_train, float), batch_size=batch_size),
output_types=(tf.float32, tf.float32),
output_shapes =(tf.TensorShape([None, int(settings["image_height"]), int(settings["image_width"]), 1]), tf.TensorShape([None, int(len(classes))]))
).repeat()#.shuffle(len(X_train), reshuffle_each_iteration=True)
- #dataset = tf.data.Dataset.from_tensor_slices((tf.cast(X_train, float), Y_train)).batch(batch_size)
+
#dataset = datagen.flow(tf.cast(X_train, float), Y_train, batch_size=batch_size)
TRex.log("tf.data.Dataset: "+str(dataset))
+ TRex.log("tf.data.Dataset (validation): "+str(validation_data))
history = model.fit(dataset,
validation_data=validation_data,
steps_per_epoch=per_epoch,
diff --git a/conda/build_conda_package.sh b/conda/build_conda_package.sh
index 141d1962185b9349a28a9b463e0eb9879be79855..263757472e4a97a20b3a7b9d2f68135a2b852606 100755
--- a/conda/build_conda_package.sh
+++ b/conda/build_conda_package.sh
@@ -1,5 +1,5 @@
if [ "$(uname)" == "Linux" ]; then
- conda build . -c main -c conda-forge
+ conda build .
else
conda build .
fi
diff --git a/conda/meta.yaml b/conda/meta.yaml
index c4548bec0d16b7a9cbc27b7a0b9a2d8bba4fc5be..df55da89664db8ee05729d9be1bf77fbc95948f8 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -17,15 +17,13 @@ source:
build:
script_env:
- GITHUB_WORKFLOW
- number: 16
+ number: 17
string: "{{ hash }}_{{ number }}"
run_exports:
- {{ pin_compatible('ffmpeg', min_pin='x.x.x', max_pin='x.x.x') }}
- {{ pin_compatible('python', min_pin='x.x.x', max_pin='x.x.x') }}
- {{ pin_compatible('libgcc-ng', min_pin='x.x.x', max_pin='x.x.x') }} # [linux]
- {{ pin_compatible('libstdcxx-ng', min_pin='x.x.x', max_pin='x.x.x') }} # [linux]
- ignore_run_exports:
- - xorg-libxinerama
detect_binary_files_with_prefix: True
files_with_prefix:
- bin/trex
@@ -48,10 +46,6 @@ requirements:
- {{ compiler('cxx') }}
- cmake >=3.14
- git
- - xorg-libxcursor # [linux]
- - xorg-libx11 # [linux]
- - xorg-libxrandr # [linux]
- - xorg-libxinerama # [linux]
- {{ cdt('mesa-libgl-devel') }} # [linux]
- {{ cdt('mesa-dri-drivers') }} # [linux]
- {{ cdt('libselinux') }} # [linux]
@@ -95,7 +89,6 @@ requirements:
- python # [not arm64]
- python=3.8 # [osx and arm64]
- nomkl # [osx]
- - xorg-libx11 # [linux]
- grpcio # [arm64]
- h5py # [arm64]
- ipython # [arm64]
diff --git a/docs/install.rst b/docs/install.rst
index 2461970e875b3c8d092c5693ea78f41925e430b6..cf6f2c6caccf56cd539ff4c5d801a8d7674fa80f 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -17,8 +17,7 @@ The easy way (Windows, Linux and Intel macOS)
|trex| supports all major platforms. There is an easy way to install |trex| using Anaconda, by creating a new virtual environment (here named ``tracking``, which you can replace)::
- conda create -n tracking -c trexing trex # macOS (Intel), Windows
- conda create -n tracking -c main -c conda-forge -c trexing trex # Linux (Intel)
+ conda create -n tracking -c trexing trex # macOS (Intel), Windows, Linux
The down-side is that pre-built binaries are compiled with fewer optimzations and features than a manually compiled one (due to compatibility and licensing issues) and thus are slightly slower =(. For example, the conda version does not offer support for Basler cameras. If you need to use |grabs| with machine vision cameras, or need as much speed as possible/the newest version, please consider compiling the software yourself.
@@ -68,8 +67,7 @@ This runs ``conda build .``, which builds the program according to all the setti
After compilation was successful, |trex| can be installed using::
- conda create -n tracking -c trexing trex # macOS, Windows
- conda create -n tracking -c main -c conda-forge -c trexing trex # Linux (Intel)
+ conda create -n tracking -c trexing trex # macOS, Windows, Linux (Intel)
Notice there is a ``-c local``, instead of the ``-c trexing`` from the first section.
@@ -94,7 +92,7 @@ As well as the general requirements:
The easiest way to ensure that all requirements are met, is by using conda to create a new environment::
- conda create -n tracking -c conda-forge cmake ffmpeg tensorflow=2 cxx-compiler c-compiler glfw mesa-libgl-devel-cos6-x86_64 libxdamage-devel-cos6-x86_64 libxi-devel-cos6-x86_64 libxxf86vm-cos6-x86_64 libselinux-devel-cos6-x86_64 libuuid-devel-cos6-x86_64 mesa-libgl-devel-cos6-x86_64
+ conda create -n tracking cmake ffmpeg tensorflow=2 cxx-compiler c-compiler mesa-libgl-devel-cos6-x86_64 libxdamage-devel-cos6-x86_64 libxi-devel-cos6-x86_64 libxxf86vm-cos6-x86_64 libselinux-devel-cos6-x86_64 libuuid-devel-cos6-x86_64 mesa-libgl-devel-cos6-x86_64
If your GPU is supported by TensorFlow, you can modify the above line by appending ``-gpu`` to ``tensorflow`` to get ``tensorflow-gpu=2``.
diff --git a/docs/parameters_trex.rst b/docs/parameters_trex.rst
index 8370d9858c2b0bb07728a9412fd1d6a52dcdb4df..de915c9324a1fc656a344f193b557e8596090d74 100644
--- a/docs/parameters_trex.rst
+++ b/docs/parameters_trex.rst
@@ -626,7 +626,7 @@ TRex parameters
.. function:: gui_interface_scale(float)
- **default value:** 0.75
+ **default value:** 1.25
Scales the whole interface. A value greater than 1 will make it smaller.
diff --git a/videos/corrected/test.settings b/videos/corrected/test.settings
new file mode 100644
index 0000000000000000000000000000000000000000..c8c65f089444a7fa3b0d23d82009781c9a15969b
--- /dev/null
+++ b/videos/corrected/test.settings
@@ -0,0 +1,7 @@
+auto_no_results = true
+blob_size_ranges = [[80,400]]
+gui_focus_group = [0]
+output_format = csv
+output_graphs = [["X",["wcentroid"]],["SPEED",["wcentroid"]],["midline_length",["RAW"]]]
+track_max_individuals = 8
+track_max_speed = 800
diff --git a/videos/test_weights.npz b/videos/corrected/test_weights.npz
similarity index 100%
rename from videos/test_weights.npz
rename to videos/corrected/test_weights.npz
diff --git a/videos/test.pv b/videos/test.pv
index 5cd56e904c8b8fed46a42b42758445291a9e81cd..97d1b6da91007a74a88f7c0e5780caad5753181d 100644
Binary files a/videos/test.pv and b/videos/test.pv differ