.gitlab-ci.yml

@@ -28,29 +28,29 @@ flake8:
     - passoft
   stage: Build Env and Test
   script:
-    - flake8 --exclude sohstationviewer/view/ui,sohstationviewer/controller/core/ sohstationviewer
+    - flake8 --exclude sohstationviewer/view/ui,sohstationviewer/controller/core/,sohstationviewer/main.py
     - flake8 tests
 
-python3.7:
-  image: python:3.7
+python3.9:
+  image: python:3.9
   tags:
     - passoft
   stage: Build Env and Test
   script:
     - python -m unittest
 
-python3.8:
-  image: python:3.8
+python3.10:
+  image: python:3.10
   tags:
     - passoft
   stage: Build Env and Test
   script:
     - python -m unittest
 
-python3.9:
-  image: python:3.9
+python3.11:
+  image: python:3.11
   tags:
     - passoft
   stage: Build Env and Test
   script:
-    - python -m unittest
+  - python -m unittest

AUTHORS.rst

+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* EPIC <software-support@passcal.nmt.edu>
+
+Contributors
+------------
+
+None yet. Why not be the first?

CONTRIBUTING.rst

+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://git.passcal.nmt.edu/software_public/passoft/sohstationviewer/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitLab issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+SOHViewer could always use more documentation, whether as part of the
+official SOHViewer docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at
+https://git.passcal.nmt.edu/software_public/passoft/sohstationviewer/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `rt2ms` for local development.
+
+1. Clone the `rt2ms` repo:
+
+ * $ git clone https://git.passcal.nmt.edu/software_public/passoft/sohstationviewer.git
+
+2. Install your local copy:
+
+ * $ pip install -e .[dev]
+
+3. Create a branch for local development:
+
+ * $ git checkout -b name-of-your-bugfix-or-feature
+
+ Now you can make your changes locally.
+
+4. When you're done making changes, check that your changes pass the
+   tests:
+
+ * $ python -m unittest
+
+5. Commit your changes and push your branch to GitHub:
+
+ * $ git add .
+ * $ git commit -m "Your detailed description of your changes."
+ * $ git push origin name-of-your-bugfix-or-feature
+
+6. Submit a merge request through the Gitlab website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a merge request, check that it meets these guidelines:
+
+1. The merge request should include tests.
+2. If the merge request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.[9,10,11]
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed.
+Then run:
+
+* $ git push
+* $ git push --tags

HISTORY.rst

@@ -2,7 +2,12 @@
 History
 =======
 
-2021.xxx
+2023.1.0.0
 --------
 
 * First release
+
+2023.1.0.1
+--------
+
+* Fixed a problem with SOHViewer not fitting on smaller resolutions

LICENSE

+GNU GENERAL PUBLIC LICENSE
+                      Version 3, 29 June 2007
+
+    Visualize State-of-Health packets from raw data recorded by different
+    type of dataloggers.
+    Copyright (C) 2018  IRIS PASSCAL
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

MANIFEST.in

+include HISTORY.rst
+include README.rst
+include sohstationviewer/database/soh.db
+
+graft sohstationviewer/documentation
+graft sohstationviewer/images
+
+recursive-exclude * __pycache__
+recursive-exclude * sohstationviewer/__pycache__
+recursive-exclude * *.py[co]

README.rst

@@ -8,43 +8,6 @@ Description
   Visualize State-of-Health packets from raw data recorded by different type of dataloggers.
 
 
-Directory Structure
--------------------
-
-    sohstationviewer/
-        model/
-            core/
-        view/
-            core/
-            ui/
-        controller/
-            core/
-
-    tests/
-
-
-Directory Description
----------------------
-
-  **sohstationviewer/**
-     All codes for running sohstationviewer.
-
-  **sohstationviewer/model/**
-     Codes for reading data from raw files and setting data from config files.
-
-  **sohstationviewer/view/**
-     Codes for Graphical User Interface (GUI).
-
-  **sohstationviewer/view/ui/**
-     ui files from QtDesigner.
-
-  **sohstationviewer/controller/**
-     Codes for logical processes.
-
-  **tests/**
-     Unittest files for the codes. (GUI will not be tested)
-
-
 License
 -------
   GNU General Public License v3 (GPLv3)

conda.recipe/meta.yaml

+package:
+  name: sohviewer
+  version: 2023.1.0.1
+
+source:
+  path: ../
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . --no-deps -vv
+
+requirements:
+  build:
+    - python >=3.9
+    - pip
+  run:
+    - python >=3.9
+    - numpy>=1.23.0
+    - obspy >=1.3.0
+    - PySide6>=6.5.2
+    - matplotlib>=3.5.0
+
+test:
+  source_files:
+    - tests
+    - sohstationviewer/database/soh.db
+  commands:
+    - python -m unittest
+
+about:
+  home: https://www.passcal.nmt.edu/content/software-resources
+  dev_url: https://git.passcal.nmt.edu/software_public/passoft/sohstationviewer
+  license: GPLv3
+  license_file: LICENSE
+  summary: Visualize State-of-Health packets from raw data recorded by different type of dataloggers.

documentation/05 _ Read from Data Card.help.md

-## To read data from data card:
-Different kinds of data card: SD card,  CF card or flash drive
-
-To read data from data card,  check the checkbox "From Data Card".
-
-File List box will display "Data Card" and the data in the selected card can be
-read without selecting "Data Card" in the box. 
-
-<br />
-<br />
-<img alt="From Data Card checkbox" src="images/data_card/from_data_card_checkbox.png" height="80" />
-<br />
-
-Note: This will work the same way as selecting the current folder nested in
-the first level of a data set.
-
-### Baler data
-Baler data has data/ folder for main data and sdata/ folder for backup
-data.  When Baler data is selected,  the radio buttons for data/ and sdata/
-are enable for user to select one of the folder to read from.
-
-<br />
-<br />
-<img alt="data/sdata radio buttons" src="images/data_card/data_sdata_radio_buttons.png" height="80" />
-<br />
-
-### CF card
-When CF card is selected,  the serial numbers of the DASs in the CF card will
-be listed for user to select for reading.
-
-<br />
-<br />
-<img alt="DAS in CF Card" src="images/data_card/das_in_cf_card.png" height="100" />
-<br />
-
-Note: DASs list will be displayed in the File List box no matter the From Data
-Card checkbox is checked or not.
\ No newline at end of file

setup.py

@@ -20,25 +20,28 @@ setup(
         'Intended Audience :: Developers',
         'License :: OSI Approved ::  GNU General Public License v3 (GPLv3)',
         'Natural Language :: English',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
+        'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: 3.11',
     ],
     description="Visualize State-of-Health packets from raw data recorded by "
                 "different type of dataloggers.",
     entry_points={
         'console_scripts': [
-            'sohstationviewer=sohstationviewer.sohstationviewer:main',
+            'sohviewer=sohstationviewer.main:main',
         ],
     },
-    install_requires=['obspy',
-                      'PySide6',
-                      'matplotlib',
-                      'numpy'],
+    install_requires=[
+        'numpy>=1.23.0',
+        'obspy>=1.3.0',
+        'PySide6>=6.5.2',
+        'matplotlib>=3.5.0',
+    ],
     setup_requires=[],
     extras_require={
         'dev': [
-            'flake8'
+            'flake8',
+            'tox'
         ]
     },
     license="GNU General Public License v3",
@@ -46,8 +49,8 @@ setup(
     include_package_data=True,
     keywords='sohstationviewer',
     name='sohstationviewer',
-    packages=find_packages(include=['sohstationviewer']),
-    url='https://git.passcal.nmt.edu/passoft/sohstationviewer',
-    version='2021.167',
+    packages=find_packages(include=['sohstationviewer*']),
+    url='https://git.passcal.nmt.edu/software_public/passoft/sohstationviewer',
+    version='2023.1.0.1',
     zip_safe=False,
 )

sohstationviewer.py

-#!/usr/bin/env python3
-import platform
-import os
-import sys
-import traceback
-
-from PySide6 import QtWidgets
-from PySide6.QtWidgets import QMessageBox, QErrorMessage
-
-from sohstationviewer.view.main_window import MainWindow
-from sohstationviewer.conf.config_processor import (
-    ConfigProcessor,
-    BadConfigError,
-)
-
-
-def main():
-    app = QtWidgets.QApplication(sys.argv)
-    wnd = MainWindow()
-    config = ConfigProcessor()
-    config.load_config()
-    need_reset = False
-    try:
-        config.validate_config()
-        config.apply_config(wnd)
-    except (BadConfigError, ValueError) as e:
-        bad_config_dialog = QMessageBox()
-        bad_config_dialog.setText('Something went wrong when reading the '
-                                  'config.')
-        bad_config_dialog.setDetailedText(traceback.format_exc())
-        bad_config_dialog.setInformativeText('Do you want to reset the config '
-                                             'file?')
-        bad_config_dialog.setStandardButtons(QMessageBox.Ok |
-                                             QMessageBox.Close)
-        bad_config_dialog.setDefaultButton(QMessageBox.Ok)
-        bad_config_dialog.setIcon(QMessageBox.Critical)
-        reset_choice = bad_config_dialog.exec_()
-        if reset_choice == QMessageBox.Ok:
-            need_reset = True
-        else:
-            sys.exit(1)
-    if need_reset:
-        try:
-            config.reset()
-        except OSError:
-            QMessageBox.critical(None, 'Cannot reset config',
-                                 'Config file cannot be reset.  Please '
-                                 'ensure that it is not opened in another '
-                                 'program.',
-                                 QMessageBox.Close)
-            sys.exit(1)
-    config.apply_config(wnd)
-    wnd.show()
-    sys.exit(app.exec())
-
-
-if __name__ == '__main__':
-    main()

sohstationviewer/conf/config_processor.py

@@ -13,6 +13,7 @@ default_config = f'''
 from_data_card = False
 data = False
 sdata = False
+log = False
 
 [ColorMode]
 black = True
@@ -48,6 +49,7 @@ to_date = {QtCore.QDate.currentDate().toString("yyyy-MM-dd")}
 mp_color_mode = regular
 tps_color_mode = High
 date_mode = YYYY-MM-DD
+add_mass_pos_to_soh = False
 '''
 
 
@@ -62,7 +64,7 @@ class ConfigProcessor:
     def __init__(self):
         self.config = configparser.ConfigParser()
         self.expected_keys = {
-            'from_data_card', 'data', 'sdata',
+            'from_data_card', 'data', 'sdata', 'log',
             'black', 'white',
             'min_gap_length',
             'mp123zne', 'mp456uvw',
@@ -71,7 +73,8 @@ class ConfigProcessor:
             'plot_tps', 'plot_raw',
             'all_soh',
             'from_date', 'to_date',
-            'mp_color_mode', 'tps_color_mode', 'date_mode'
+            'mp_color_mode', 'tps_color_mode', 'date_mode',
+                'add_mass_pos_to_soh'  # noqa: E131
         }
 
     def load_config(self):
@@ -79,7 +82,7 @@ class ConfigProcessor:
         Load the config file if there is one, otherwise load the default
         config.
         """
-        config_path = Path('sohstationviewer/conf/read_settings.ini')
+        config_path = Path('conf/read_settings.ini')
         if not config_path.exists():
             self.config.read_string(default_config)
         else:
@@ -109,10 +112,16 @@ class ConfigProcessor:
                 f'missing keys are: {", ".join(missing_keys)}'
             )
 
+        from_data_card_checked = self.config.getboolean('FileRead',
+                                                        'from_data_card')
         data_checked = self.config.getboolean('FileRead', 'data')
         sdata_checked = self.config.getboolean('FileRead', 'sdata')
+        log_checked = self.config.getboolean('FileRead', 'log')
         if data_checked and sdata_checked:
             raise BadConfigError('data and sdata cannot both be chosen.')
+        if from_data_card_checked and log_checked:
+            raise BadConfigError('Cannot read from data card and log file at '
+                                 'the same time.')
 
         black_color_mode = self.config.getboolean('ColorMode', 'black')
         white_color_mode = self.config.getboolean('ColorMode', 'white')
@@ -187,6 +196,7 @@ class ConfigProcessor:
         )
         window.data_radio_button.setChecked(get_bool('FileRead', 'data'))
         window.sdata_radio_button.setChecked(get_bool('FileRead', 'sdata'))
+        window.log_checkbox.setChecked(get_bool('FileRead', 'log'))
 
         window.background_black_radio_button.setChecked(
             get_bool('ColorMode', 'black')
@@ -253,6 +263,10 @@ class ConfigProcessor:
         elif date_mode == 'YYYY:DOY':
             window.yyyy_doy_action.trigger()
 
+        window.add_masspos_to_rt130_soh.setChecked(
+            get_bool('MiscOptions', 'add_mass_pos_to_soh')
+        )
+
     def reset(self):
         self.config = configparser.ConfigParser()
         self.config.read_string(default_config)

sohstationviewer/conf/constants.py

-import sys
-if sys.version_info.minor >= 8:
-    from typing import Literal
+from typing import Literal
+
+# The current version of SOHStationViewer
+SOFTWARE_VERSION = '2023.1.0.1'
 
 # waveform pattern
 WF_1ST = 'A-HLM-V'
@@ -11,7 +12,7 @@ WF_3RD = 'ZNE123456'
 HIGHEST_INT = 1E100
 
 # warn user if file bigger than this size
-BIG_FILE_SIZE = 2 * 10**8
+BIG_FILE_SIZE = 2 * 10**9       # 2 GB
 
 # Matplotlib's performance be slow if data point total > than this limit
 CHAN_SIZE_LIMIT = 10**6
@@ -53,11 +54,12 @@ SEARCH_RESULTS = "Search Results.md"
 ALL_COLOR_MODES = {'B': 'black', 'W': 'white'}
 
 # The location of the config file
-CONFIG_PATH = 'sohstationviewer/conf/read_settings.ini'
+CONFIG_PATH = 'conf/read_settings.ini'
 
 # List of image formats. Have to put PNG at the beginning to go with
 # dpi in dialog
 IMG_FORMAT = ['PNG', 'PDF', 'EPS', 'SVG']
+
 # ================================================================= #
 #                      PLOTTING CONSTANT
 # ================================================================= #
@@ -74,11 +76,10 @@ Z_ORDER = {'AXIS_SPINES': 0, 'CENTER_LINE': 1, 'LINE': 2, 'GAP': 3, 'DOT': 3}
 # Distance from 'Hour' label to timestamp bar
 HOUR_TO_TMBAR_D = 100
 
+# day total limit for all tps channels to stay in one tab
+DAY_LIMIT_FOR_TPS_IN_ONE_TAB = 180      # about half of a year
 # ================================================================= #
 #                      TYPING CONSTANT
 # ================================================================= #
 
-if sys.version_info.minor >= 8:
-    ColorMode = Literal['B', 'W']
-else:
-    ColorMode = str
+ColorMode = Literal['B', 'W']

sohstationviewer/conf/dbSettings.py

 import re
+import os
+from pathlib import Path
 
 from sohstationviewer.conf.constants import (WF_1ST, WF_2ND, WF_3RD)
 """
@@ -10,7 +12,7 @@ Third letter (Orientation Code): ZNE123
 """
 
 dbConf = {
-    'dbpath': 'sohstationviewer/database/soh.db',
+    'dbpath': 'database/soh.db',
     'seisRE': re.compile(f'[{WF_1ST}][{WF_2ND}][{WF_3RD}]'),
     # key is last char of chan
     'seisLabel': {'1': 'NS', '2': 'EW', 'N': 'NS', 'E': 'EW', 'Z': 'V'},
@@ -42,3 +44,20 @@ dbConf = {
             "If D is not defined, dots won't be displayed.\n"
             "If L is not defined, lines will be plotted with color G")}
 }
+
+
+def modify_db_path():
+    """
+    Modify dbpath to absolute path.
+
+    This function is called in case database needs to be used when the working
+    directory is a sub folder of root, sohstationviewer/. The following lines
+    need to be added:
+        from sohstationviewer.conf.dbSettings import modify_db_path
+        modify_db_path()
+    """
+    global dbConf
+    current_file_path = os.path.abspath(__file__)
+    root = Path(current_file_path).parent.parent
+    db_path = [x for x in root.glob('**/soh.db')][0]
+    dbConf['dbpath'] = db_path.as_posix()

sohstationviewer/controller/plotting_data.py

 """
 Functions that process data for plotting
 """
-
 import math
 from typing import List, Union, Optional, Tuple, Dict
 
 from obspy import UTCDateTime
 
 from sohstationviewer.conf import constants as const
-from sohstationviewer.view.util.enums import LogType
+
 
 MAX_INT = 1E100
 MAX_FLOAT = 1.0E100
 
-# TODO: put this in DB
-mass_pos_volt_ranges = {"regular": [0.5, 2.0, 4.0, 7.0],
-                        "trillium": [0.5, 1.8, 2.4, 3.5]}
-mass_pos_color_pallets = {"B": ["C", "G", "Y", "R", "M"],
-                          "W": ["B", "B", "B", "B", "B"]}
-
-
-def get_masspos_value_colors(
-        range_opt: str, chan_id: str, c_mode: str,
-        processing_log: List[Tuple[str, LogType]],
-        ret_type: str = 'str'
-) -> Optional[Union[str, List[Tuple[float, str]]]]:
-    """
-    Create a map between value and color based on given rangeOpt and c_mode to
-    display mass position plots.
-    :param range_opt: massPosVoltRangeOpt got from Options Menu - MP coloring
-        in Main Window to define different values for mass position.
-        (regular/trillium)
-    :param chan_id: ID of the channel
-    :param c_mode: color mode (B/W)
-    :param processing_log: list of processing info and type
-    :param ret_type: request return type
-    :return: [(value, color), (value, color) ...]
-        if retType is 'str', return "value:color|value:color"
-    """
-
-    if range_opt.lower() not in mass_pos_volt_ranges.keys():
-        processing_log.append(
-            (
-                f"{chan_id}: The current selected Mass Position color range is"
-                f" '{range_opt}' isn't allowable. The accept ranges are: "
-                f"{', '.join(mass_pos_volt_ranges.keys())}",
-                LogType.ERROR
-            )
-        )
-        return
-    mass_pos_volt_range = mass_pos_volt_ranges[range_opt]
-    mass_pos_color_pallet = mass_pos_color_pallets[c_mode]
-    value_colors = []
-    for i in range(len(mass_pos_volt_range)):
-        if ret_type == 'str':
-            value_colors.append(
-                "%s:%s" % (mass_pos_volt_range[i], mass_pos_color_pallet[i]))
-        else:
-            value_colors.append(
-                (mass_pos_volt_range[i], mass_pos_color_pallet[i])
-            )
-        if i == len(mass_pos_volt_range) - 1:
-            if ret_type == 'str':
-                value_colors.append(
-                    "%s:+%s" % (
-                        mass_pos_volt_range[i], mass_pos_color_pallet[i + 1]))
-            else:
-                value_colors.append(
-                    (mass_pos_volt_range[i], mass_pos_color_pallet[i + 1]))
-    if ret_type == 'str':
-        return '|'.join(value_colors)
-    return value_colors
-
 
 def format_time(time: Union[UTCDateTime, float], date_mode: str,
                 time_mode: Optional[str] = None) -> str: