Merge pull request #98 from Any2HRTF/develop

Release 1.1.0

CONTRIBUTING.rst

@@ -104,12 +104,11 @@ Releasing
 To release a new Mesh2HRTF version do the following
 
 - Write the new version to the file VERSION and mesh2input.py
-- Update HISTORY.rst (also include new contributors)
 - Commit all changes to develop
-- merge develop into main
+- Update HISTORY.rst (also include new contributors)
 - check if the tests pass
 - check if the documentation is building
 - check if installing the python package works via ``pip install -e .``
-- add a tag with the version number ``git tag <tagname>``, e.g. ``git tag v1.0.0``
-- push the tag using ``git push origin --follow-tags``
-- add a release on github
+- merge develop into main
+- add a tagg and release on github
+- merge main into develop

Dockerfile

@@ -0,0 +1,67 @@
+# This Dockerfile can be used to run Mesh2HRTF inside a Docker container.
+# Some information on how the container can be generated are given below. For
+# more information refer to docker.com
+#
+# Inside the container you can
+# - Run the `hrtf_mesh_grading`
+# - Run numerical simualtions with the `NumCalc` command
+# - Access the Mesh2HRTF Python API, e.g. by running `python3` and then
+#   `import mesh2hrtf`
+#
+# You can build the container in the command line by executing
+# `docker build --tag ubuntu:mesh2hrtf .` (without the ` signs)
+#
+# Start the container with out an external volume with:
+# `docker run -dit --name mesh2hrtf ubuntu:mesh2hrtf /bin/bash`
+#
+# Start the container with an external volume mounted at /home/data:
+# `docker run -dit --name mesh2hrtf -v '/local/folder:/home/data' ubuntu:mesh2hrtf /bin/bash`
+
+FROM ubuntu:22.04
+
+# All commands are run from this path
+WORKDIR /home
+
+# Configure tzdata and timezone if problems appear during `apt-get install cmake`
+#ENV TZ=Europe/Berlin
+#RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+# install required dependencies (remove specific versions if desired)
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive apt-get upgrade -y
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y cmake \
+                   make \
+                   build-essential\
+                   libx11-dev \
+                   libxrandr-dev \
+                   libxinerama-dev \
+                   libxcursor-dev \
+                   libxi-dev \
+                   libgl1-mesa-dev \
+                   libglu1-mesa-dev \
+                   libeigen3-dev \
+                   python3 \
+                   python3-pip
+
+# copy Mesh2HRTF git repo to docker container
+COPY . /home/Mesh2HRTF
+
+# install Mesh2HRTF Python API
+RUN pip install -e /home/Mesh2HRTF
+
+# build NumCalc
+RUN cd /home/Mesh2HRTF/mesh2hrtf/NumCalc/src && make
+
+# add symbolic linc for NumCalc
+RUN ln -s /home/Mesh2HRTF/mesh2hrtf/NumCalc/bin/NumCalc /usr/local/bin
+
+# build the pmp-library
+RUN cd /home/Mesh2HRTF/mesh2hrtf/Mesh2Input/Meshes/GradingHybrid/pmp-library \
+    && mkdir build && cd build && cmake .. && make && make install
+
+# add libpmp to the search path
+RUN echo /usr/local/lib > /etc/ld.so.conf.d/local.conf
+RUN ldconfig
+
+# add symbolic link for hrtf-mesh-grading
+RUN ln -s /home/Mesh2HRTF/mesh2hrtf/Mesh2Input/Meshes/GradingHybrid/pmp-library/build/hrtf_mesh_grading /usr/local/bin

HISTORY.rst

@@ -1,9 +1,12 @@
 History
 =======
 
-v1.0.1 (7 Mai 2023)
+v1.1.0 (11 Mai 2023)
 -------------------
+* Add dockerfile running the Mesh2HRTF Python API, `NumCalc`, and `hrtf_mesh_grading`
 * Fixed a bug in installing the Mesh2HRTF Python API
+* Fixed a bug in `manage_numcalc` if running multiple Mesh2HRTF projects
+* Fix order of HRIRs/HRTFs plotted by `inspect_sofa_files` when choosing the median or frontal plane
 
 v1.0.0 (28 April 2023)
 ----------------------

VERSION

@@ -1 +1 @@
-1.0.1
+1.1.0

docs/conf.py

@@ -71,7 +71,7 @@
 #
 # The short X.Y version.
 with open(os.path.join('..', 'VERSION')) as version_file:
-    version = version_file.read()
+    version = version_file.read().strip()
 # The full version, including alpha/beta/rc tags.
 release = version
 

mesh2hrtf/Mesh2Input/mesh2input.py

@@ -302,7 +302,7 @@ def save(operator,
 
         # get Mesh2HRTF version
         with open(os.path.join(programPath, "..", "VERSION")) as read_version:
-            version = read_version.readline()
+            version = read_version.readline().strip()
 
         # Export path and export directory handling
         if not filepath.endswith(os.path.sep):

mesh2hrtf/NumCalc/manage_numcalc.py

@@ -97,8 +97,12 @@ def manage_numcalc(project_path=os.getcwd(), numcalc_path=None,
         numcalc_path = "NumCalc" if numcalc_path is None else numcalc_path
 
     ram_info = psutil.virtual_memory()
-    max_ram_load = ram_info.total / 1073741824 \
-        if max_ram_load is None else max_ram_load
+    if max_ram_load is None:
+        max_ram_load = ram_info.total / 1073741824
+    elif max_ram_load > ram_info.total / 1073741824:
+        raise ValueError((
+            f"The maximum RAM load of {max_ram_load} GB must be smaller than "
+            f"the total RAM, which is {ram_info.total / 1073741824} GB."))
 
     # helping variables -------------------------------------------------------
 
@@ -268,13 +272,12 @@ def manage_numcalc(project_path=os.getcwd(), numcalc_path=None,
 
         # check if available memory is enough for running the instance with the
         # highest memory consumption without ever exceeding 100% of RAM.
-        ram_available, ram_used = _get_current_ram(ram_offset)
-        if ram_available < instances_to_run[-1, 3] * ram_safety_factor:
+        if max_ram_load < instances_to_run[-1, 3] * ram_safety_factor:
             # note: it IS possible to run simulations that use even more than
             # 100% of available system RAM - only the performance will be poor.
             _raise_error((
                 f"Stop - not sufficient free RAM for this simulation project: "
-                f"Available RAM is {round(ram_available, 2)} GB, but frequency"
+                f"Available RAM is {round(max_ram_load, 2)} GB, but frequency"
                 f" step {int(instances_to_run[-1, 1])} of source "
                 f"{int(instances_to_run[-1, 0])} requires "
                 f"{round(instances_to_run[-1, 3] * ram_safety_factor, 2)} "

mesh2hrtf/Output2HRTF/inspect_sofa_files.py

@@ -204,7 +204,7 @@ def _inspect_sofa_files(file, savedir, atol, plot, plane,
 
             if not np.any(mask):
                 warnings.warn((
-                    "Did not find and sources on the horizontal plane for "
+                    f"Did not find and sources on the {plane} plane for "
                     f"within +/-{atol} deg. for {file}"))
                 return
 
@@ -218,7 +218,8 @@ def _inspect_sofa_files(file, savedir, atol, plot, plane,
                 # plot time data
                 if mode == "hrir":
                     _, qm, _ = pf.plot.time_2d(
-                        signal[mask, cc], indices=angles, dB=dB_time,
+                        signal[mask, cc][np.argsort(angles)],
+                        indices=np.sort(angles), dB=dB_time,
                         ax=ax_time[cc], cmap="coolwarm")
                     ax_time[cc].set_title(name)
 
@@ -230,7 +231,8 @@ def _inspect_sofa_files(file, savedir, atol, plot, plane,
 
                 # plot frequency data
                 _, qm, _ = pf.plot.freq_2d(
-                    signal[mask, cc], ax=ax_freq[cc], indices=angles,
+                    signal[mask, cc][np.argsort(angles)],
+                    indices=np.sort(angles), ax=ax_freq[cc],
                     dB=dB_freq, freq_scale=freq_scale, cmap="Reds")
                 if mode == "hrir":
                     ax_freq[cc].set_xlabel(f"{angle} in degree")
@@ -245,5 +247,6 @@ def _inspect_sofa_files(file, savedir, atol, plot, plane,
 
             # save
             plt.tight_layout()
-            plt.savefig(os.path.join(savedir, tail[:-5] + "_3D.jpeg"),
-                        dpi=300, bbox_inches="tight")
+            plt.savefig(
+                os.path.join(savedir, f"{tail[:-5]}_3D_{plane}_plane.jpeg"),
+                dpi=300, bbox_inches="tight")

setup.py

@@ -12,7 +12,7 @@
     history = history_file.read()
 
 with open('VERSION') as version_file:
-    version = version_file.read()
+    version = version_file.read().strip()
 
 requirements = [
     'numpy>=1.14.0',

tests/test_output.py

@@ -1,7 +1,8 @@
+import matplotlib as mpl
+import matplotlib.pyplot as plt
 import pytest
 import numpy as np
 import numpy.testing as npt
-import matplotlib.pyplot as plt
 from tempfile import TemporaryDirectory
 import shutil
 import os
@@ -11,6 +12,8 @@
 import sofar as sf
 import mesh2hrtf as m2h
 
+mpl.use('Agg')
+
 cwd = os.path.dirname(__file__)
 data_shtf = os.path.join(cwd, 'resources', 'SHTF')
 data_nc = os.path.join(cwd, 'resources', 'nc.out')
@@ -104,8 +107,9 @@ def test_output_two_hrtf_and_Output2HRTF(num_sources):
     ["HRIR", "2D", ["HRIR_*_2D"], ["HRIR_*_3D", "HRTF_*_2D", "HRTF_*_3D"]],
     ["HRIR", "3D", ["HRIR_*_3D"], ["HRIR_*_2D", "HRTF_*_2D", "HRTF_*_3D"]]
 ))
+@pytest.mark.parametrize("plane", ('horizontal', 'median', 'frontal'))
 def test_inspect_sofa_files_single_project(
-        pattern, plot, created, not_created):
+        pattern, plot, created, not_created, plane):
     """
     Test if inspect_sofa_files creates the correct plots for a single project.
     Note: Not all options for reading from and saving to different directories
@@ -123,20 +127,28 @@ def test_inspect_sofa_files_single_project(
         os.remove(file)
 
     # create plots
-    m2h.inspect_sofa_files(tmp_shtf, pattern, plot=plot)
+    m2h.inspect_sofa_files(tmp_shtf, pattern, plot=plot, plane=plane)
 
     grid = "FourPointHorPlane_r100cm"
 
     # check if the correct files exist and are missing
     for file in created:
         file = os.path.join(tmp_shtf, "Output2HRTF", file.replace("*", grid))
-        extension = ".pdf" if "2D" in file else ".jpeg"
-        assert os.path.isfile(file + extension)
+        if "2D" in file:
+            file_name = f"{file}.pdf"
+        else:
+            file_name = f"{file}_{plane}_plane.jpeg"
+        assert os.path.isfile(file_name)
 
     for file in not_created:
         file = os.path.join(tmp_shtf, "Output2HRTF", file.replace("*", grid))
-        extension = ".pdf" if "2D" in file else ".jpeg"
-        assert not os.path.isfile(file + extension)
+        if "2D" in file:
+            file_name = f"{file}.pdf"
+        else:
+            file_name = f"{file}_{plane}_plane.jpeg"
+        assert not os.path.isfile(file_name)
+
+    plt.close('all')
 
 
 def test_compute_hrir_custom_sampling_rate():

tests/test_outputs.py

@@ -5,6 +5,9 @@
 from glob import glob
 from tempfile import TemporaryDirectory
 import mesh2hrtf as m2h
+import matplotlib as mpl
+
+mpl.use("Agg")
 
 cwd = os.path.dirname(__file__)
 data_shtf = join(cwd, 'resources', 'SHTF')
@@ -109,10 +112,10 @@ def test_outputs_to_hrtfs_full():
     output = [os.path.basename(o) for o in output]
     files = ["HRTF_HRIR_FourPointHorPlane_r100cm.sofa",
              "HRTF_HRIR_FourPointHorPlane_r100cm_2D.pdf",
-             "HRTF_HRIR_FourPointHorPlane_r100cm_3D.jpeg",
+             "HRTF_HRIR_FourPointHorPlane_r100cm_3D_horizontal_plane.jpeg",
              "SHTF_HRIR_FourPointHorPlane_r100cm.sofa",
              "SHTF_HRIR_FourPointHorPlane_r100cm_2D.pdf",
-             "SHTF_HRIR_FourPointHorPlane_r100cm_3D.jpeg"]
+             "SHTF_HRIR_FourPointHorPlane_r100cm_3D_horizontal_plane.jpeg"]
     assert len(output) == len(files)
     for file in files:
         assert file in output

tests/test_tutorials.py

@@ -80,11 +80,10 @@ def test_tutorials(tutorial):
         cwd=tmp.name, check=True, capture_output=True)
 
     if run_numcalc:
-        # run manage_numcalc
+        # run manage_numcalc and process output
         print("running NumCalc")
         m2h.manage_numcalc(os.path.join(tmp.name, tutorial[:-3]), numcalc)
 
-        # run manage_numcalc
         print("running output2hrtf")
         m2h.output2hrtf(os.path.join(tmp.name, tutorial[:-3]))
         plt.close("all")