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fixed generation bug and typos
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@kdreher
kdreher committed Jul 29, 2024
1 parent 270e5d2 commit 442f103
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -43,6 +43,7 @@ The SIMPA path management takes care of that.
* [SIMPA installation instructions](#simpa-installation-instructions)
* [External tools installation instructions](#external-tools-installation-instructions)
* [Path Management](#path-management)
* [Testing](#run-manual-tests)

## SIMPA installation instructions

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4 changes: 4 additions & 0 deletions docs/source/introduction.md
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Expand Up @@ -7,6 +7,7 @@ The SIMPA path management takes care of that.
* [SIMPA installation instructions](#simpa-installation-instructions)
* [External tools installation instructions](#external-tools-installation-instructions)
* [Path Management](#path-management)
* [Testing](#run-manual-tests)

## SIMPA installation instructions

Expand Down Expand Up @@ -78,6 +79,9 @@ one we provided in the `simpa_examples/path_config.env.example`) in the followin

For this option, please follow the instructions in the `simpa_examples/path_config.env.example` file.

## Run manual tests
To check the success of your installation ot to assess how your contributions affect the Simpa simulation outcomes, you can run the manual tests automatically. Install the testing requirements by doing `pip install .[testing]` and run the `simpa_tests/manual_tests/generate_overview.py` file. This script runs all manual tests and generates both a markdown and an HTML file that compare your results with the reference results.

# Simulation examples

To get started with actual simulations, SIMPA provides an [example package](simpa_examples) of simple simulation
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56 changes: 31 additions & 25 deletions simpa_tests/manual_tests/generate_overview.py
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Expand Up @@ -27,9 +27,10 @@ class GenerateOverview():

def __init__(self, verbose: bool = False, save_path: str = None):
self.verbosity = verbose
self.logger= Logger()
self.logger = Logger()
self.import_path = "simpa_tests.manual_tests"
self.current_dir = os.path.dirname(os.path.realpath(__file__)) # directory of this script, i.e ~/simpa/simpa_tests/manual_tests
# directory of this script, i.e ~/simpa/simpa_tests/manual_tests
self.current_dir = os.path.dirname(os.path.realpath(__file__))
self.file_name = os.path.basename(__file__)
self.reference_figures_path = os.path.join(self.current_dir, "reference_figures/")
if save_path == None:
Expand All @@ -44,21 +45,21 @@ def __init__(self, verbose: bool = False, save_path: str = None):

# Note: Open issue in PointSourceReconstruction.py file (make it consistent with the other manual tests)
self.scripts_to_neglect = ["PointSourceReconstruction.py"]

def download_reference_images(self):
"""
Removes the current reference figures directory and downloads the latest references from nextcloud.
:return: None
"""
ref_imgs_path = os.path.join(self.current_dir,"reference_figures")
ref_imgs_path = os.path.join(self.current_dir, "reference_figures")
if os.path.exists(ref_imgs_path):
# Remove the directory
shutil.rmtree(ref_imgs_path)
# nextcloud url with the reference images
self.nextcloud_url = "https://hub.dkfz.de/s/Xb96SFXbmiE5Fk8" # shared "reference_figures" folder on nextcloud
self.nextcloud_url = "https://hub.dkfz.de/s/Xb96SFXbmiE5Fk8" # shared "reference_figures" folder on nextcloud
# Specify the local directory to save the files
zip_filepath = os.path.join(self.current_dir, "downloaded.zip")
zip_filepath = os.path.join(self.current_dir, "downloaded.zip")
# Construct the download URL based on the public share link
download_url = self.nextcloud_url.replace('/s/', '/index.php/s/') + '/download'
# Send a GET request to download the file
Expand Down Expand Up @@ -103,12 +104,12 @@ def clean_dir(self, dir):
try:
dir.remove(name)
except ValueError:
pass
pass

def log_version(self):
"""
Logs the current 'simpa' version to a file and compares it with a reference version.
:return: None
"""
self.simpa_version = version("simpa")
Expand All @@ -133,13 +134,13 @@ def log_version(self):
</table>
""")
if self.simpa_version != reference_sp_version:
self.logger.debug("Your simpa version does not match with the simpa version used for generating the reference figures")
self.logger.debug(
"Your simpa version does not match with the simpa version used for generating the reference figures")
except FileNotFoundError:
self.logger.warning(f"The reference simpa version file at {ref_version_path} was not found")
except IOError:
self.logger.warning(f"An error occurred while reading the file at {ref_version_path}")


def run_manual_tests(self, run_tests: bool = True):
"""
runs all the scripts and creates md file with the results figures
Expand All @@ -154,7 +155,7 @@ def run_manual_tests(self, run_tests: bool = True):
directories = os.listdir(self.current_dir)
directories.sort()
self.clean_dir(directories)

for dir_num, dir_ in enumerate(directories):
self.logger.debug(f"Enter dir: {dir_}")
dir_title = f"{dir_num+1}. " + dir_.replace("_", " ").capitalize()
Expand All @@ -165,18 +166,18 @@ def run_manual_tests(self, run_tests: bool = True):

# iterate through scripts
for file_num, file in enumerate(files):
self.logger.debug(f"Enter file: {file}")
self.logger.debug(f"Enter file: {file}")
test_save_path = os.path.join(self.save_path, file.split(".py")[0] + "/")
os.makedirs(test_save_path, exist_ok=True)

if file in self.scripts_to_neglect:
self.logger.debug(f"{file} has bug or is not compatible and has to be neglected")
continue

file_title = f"{dir_num+1}.{file_num+1} " + file.split(".py")[0]
self.mdFile.new_header(level=2, title=file_title)
global_path = os.path.join(self.current_dir, dir_, file)

global_path = os.path.join(self.current_dir, dir_, file)
module_name = ".".join([self.import_path, dir_, file.split(".")[0]])

# execute all manual test scripts
Expand All @@ -190,7 +191,7 @@ def run_manual_tests(self, run_tests: bool = True):
classes = [node.name for node in ast.walk(p) if isinstance(node, ast.ClassDef)]
for class_name in classes:
self.logger.debug(f"Run {class_name}")

class_ = getattr(module, class_name)

# write class documentation string in the markdown file
Expand All @@ -202,13 +203,15 @@ def run_manual_tests(self, run_tests: bool = True):
test_object = class_()
if run_tests:
if not self.verbosity:
self.deafen(test_object.run_test, show_figure_on_screen=False, save_path=test_save_path)
self.deafen(test_object.run_test, show_figure_on_screen=False,
save_path=test_save_path)
else:
test_object.run_test(show_figure_on_screen=False, save_path=test_save_path)
except Exception as e:
self.logger.warning(f"Error Name: {type(e).__name__}")
self.logger.warning(f"Error Message: {e}")
self.mdFile.write(f"\n- <font color=red><b>ERROR occured:</b></font><br>- Error: {type(e).__name__}<br>- Error message: {e}\n")
self.mdFile.write(
f"\n- <font color=red><b>ERROR occured:</b></font><br>- Error: {type(e).__name__}<br>- Error message: {e}\n")

# Write comparison of reference image and new generated image in markdown file
self.mdFile.write("\n- <b>Comparison of reference and generated image:</b><br>\n")
Expand All @@ -224,7 +227,7 @@ def run_manual_tests(self, run_tests: bool = True):
self.create_comparison_html_table(ref_img_path, img_path)
except:
self.mdFile.write("Could not load any figures.")

# Create a table of contents
self.mdFile.new_table_of_contents(table_title='Contents', depth=2)
self.logger.debug(f"Saving md file in {os.getcwd()=}")
Expand Down Expand Up @@ -269,6 +272,7 @@ def create_comparison_html_table(self, img1_path=None, img2_path=None):
</tr>
</table>
""")

def set_style(self):
"""
Writes CSS styles to the Markdown file for image and header formatting, including zoom functionality.
Expand Down Expand Up @@ -311,7 +315,7 @@ def set_style(self):
}
</style>
""")

def deafen(self, method, **kwargs):
"""
Suppresses output and logging temporarily while executing a specified method.
Expand Down Expand Up @@ -342,7 +346,8 @@ def create_html(self):
try:
self.logger.debug(f"Saving html file in {os.getcwd()=}")
with open(os.path.join(os.getcwd(), self.md_name+".html"), "w") as html_file:
text = pypandoc.convert_text(self.mdFile.get_md_text(), "html", format="md", extra_args=['--markdown-headings=atx'])
text = pypandoc.convert_text(self.mdFile.get_md_text(), "html", format="md",
extra_args=['--markdown-headings=atx'])
updated_text = ""
for row in text.split("\n"):
if 'href="#' in row:
Expand All @@ -361,13 +366,14 @@ def create_html(self):
else:
updated_text += (row+"\n")
html_file.write(updated_text)
#pypandoc.convert_file(self.md_name + ".md", 'html', outputfile=self.md_name + '.html')
# pypandoc.convert_file(self.md_name + ".md", 'html', outputfile=self.md_name + '.html')
except Exception as e:
self.logger.warning("Check installtion of needed requirements (pypandoc, pypandoc_binary).")
self.logger.warning("Check installation of needed requirements (pypandoc, pypandoc_binary).")


if __name__ == '__main__':
automatic_manual_tests = GenerateOverview()
automatic_manual_tests.download_reference_images()
automatic_manual_tests.log_version()
automatic_manual_tests.run_manual_tests(run_tests=False)
automatic_manual_tests.create_html()
automatic_manual_tests.run_manual_tests(run_tests=True)
automatic_manual_tests.create_html()

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