Merge pull request #42 from Loop3D/fix_thicknesses

feat: added thickness calculator fields

Author: AngRodrigues

.github/workflows/release.yml

@@ -6,29 +6,36 @@ permissions:
   pull-requests: write
 
 jobs:
-  # linting:
-  #   name: Linting
-  #   runs-on: ubuntu-latest
-  #   steps:
-  #     - uses: actions/checkout@v4
-  #     - name: Install dependencies
-  #       run: |
-  #         python -m pip install --upgrade pip
-  #         pip install black ruff
-  #     - name: Autoformat with black
-  #       run: |
-  #         black .
-  #     - name: Lint with ruff
-  #       run: |
-  #         ruff check LoopProjectFile --fix
-  #     - uses: stefanzweifel/git-auto-commit-action@v5
-  #       with:
-  #         commit_message: "style: style fixes by ruff and autoformatting by black"
-          
+  linting:
+    name: Linting
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black ruff
+      - name: Autoformat with black
+        run: |
+          black .
+      - name: Lint with ruff
+        run: |
+          ruff check . --fix
+      - name: Check for local changes
+        run: |
+          if [ -n "$(git status --porcelain)" ]; then
+            git config --global user.name "github-actions[bot]"
+            git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+            git add .
+            git commit -m "style: style fixes by ruff and autoformatting by black"
+          fi
+      - uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          commit_message: "style: style fixes by ruff and autoformatting by black"
 
   pip-build-sdist:
     name: Build SDist
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
 
@@ -46,7 +53,7 @@ jobs:
   pip-test-sdist:
     name: Test sdist
     needs: pip-build-sdist
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Download sdist from artifacts
         uses: actions/download-artifact@v4
@@ -70,7 +77,7 @@ jobs:
       fail-fast: false
       matrix:
         os: 
-          - ubuntu-latest
+          - ubuntu-24.04
           - macos-latest
           - windows-latest
 
@@ -98,13 +105,13 @@ jobs:
       fail-fast: false
       matrix:
         os:
-          - ubuntu-latest
+          - ubuntu-24.04
           - macos-latest
           - windows-latest
         python-version: ["3.9", "3.10", "3.11", "3.12"]
         include:
-          - os: "ubuntu-latest"
-            artifact: loopprojectfile-wheels-ubuntu-latest
+          - os: "ubuntu-24.04"
+            artifact: loopprojectfile-wheels-ubuntu-24.04
           - os: "macos-latest"
             artifact: loopprojectfile-wheels-macos-latest
           - os: "windows-latest"
@@ -146,7 +153,7 @@ jobs:
       fail-fast: false
       matrix:
         os:   
-        - ubuntu-latest
+        - ubuntu-24.04
         - macos-latest
         - windows-latest
         python-version: ["3.9", "3.10", "3.11", "3.12"]
@@ -195,7 +202,7 @@ jobs:
 
   release-please:
     needs: [pip-test-wheels, conda-build]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     if: github.ref == 'refs/heads/master'
     steps:
       - uses: actions/checkout@v4

LoopProjectFile/DataCollection.py

@@ -79,7 +79,8 @@ def CreateObservationGroup(dataCollectionGroup):
     obGroup.createDimension("foldObservationIndex", None)
     obGroup.createDimension("foliationObservationIndex", None)
     obGroup.createDimension("discontinuityObservationIndex", None)
-    obGroup.createDimension("stratigraphicObservationIndex", None)
+    obGroup.createDimension("stratigraphicObservationIndex", None)    
+    
     faultObservationType_t = obGroup.createCompoundType(
         LoopProjectFile.faultObservationType, "FaultObservation"
     )

LoopProjectFile/Extents.py

@@ -1,6 +1,5 @@
 # import netCDF4
 
-
 # Check extents of Loop Project File is valid
 def CheckExtentsValid(rootGroup, xyzGridSize, verbose=False):
     """

LoopProjectFile/ExtractedInformation.py

@@ -2,7 +2,6 @@
 import LoopProjectFile
 import LoopProjectFile.LoopProjectFileUtils as LoopProjectFileUtils
 
-# import numpy
 
 
 # Check Extracted Information valid if present
@@ -51,6 +50,14 @@ def GetStratigraphicInformationGroup(rootGroup, verbose=False):
         )
 
 
+def GetStratigraphicThicknessGroup(rootGroup, verbose=False):
+    resp = GetExtractedInformationGroup(rootGroup, verbose)
+    if resp["errorFlag"]:
+        return resp
+    else:
+        return LoopProjectFileUtils.GetGroup(resp["value"], "StratigraphicThickness", verbose)
+
+
 def GetDrillholeDescriptionGroup(rootGroup, verbose=False):
     resp = GetExtractedInformationGroup(rootGroup, verbose)
     if resp["errorFlag"]:
@@ -255,8 +262,12 @@ def GetDiscontinuityLog(root, indexList=[], indexRange=(0, 0), verbose=False):
     )
 
 
-# Set stratigraphic log
-def SetStratigraphicLog(root, data, append=False, verbose=False):
+def SetStratigraphicLog(
+    root, 
+    data, 
+    append=False, 
+    verbose=False
+):
     """
     **SetStratigraphicLog** - Saves a list of strata in (formation,
     thickness) format into the netCDF Loop Project File
@@ -267,15 +278,19 @@ def SetStratigraphicLog(root, data, append=False, verbose=False):
         The root group node of a Loop Project File
     data: list of (formation, thickness)
         The data to save
+    thickness_calculator_data: list of tuples
+        Labels for thickness calculators (e.g., [('Label1', 'Label2', ...)])
+    thickness_calculator_active_flags: list of tuples
+        Flags for active thickness calculators (e.g., [('None', 'Active', ...)])
     append: bool
         Flag of whether to append new data to existing log
     verbose: bool
         A flag to indicate a higher level of console logging (more if True)
 
     Returns
     -------
-       dict {"errorFlag", "errorString"}
-        errorString exist and contains error message only when errorFlag is
+    dict {"errorFlag", "errorString"}
+        errorString exists and contains error message only when errorFlag is
         True
 
     """
@@ -302,23 +317,28 @@ def SetStratigraphicLog(root, data, append=False, verbose=False):
             zlib=True,
             complevel=9,
         )
+
     else:
         siGroup = resp["value"]
 
     if siGroup:
         stratigraphicLayersLocation = siGroup.variables["stratigraphicLayers"]
+
         index = 0
         if append:
             index = siGroup.dimensions["index"].size
         for i in data:
             stratigraphicLayersLocation[index] = i
             index += 1
         siGroup.setncattr("index_MaxValid", index)
+
+
     else:
         errStr = "(ERROR) Failed to create stratigraphic log group for strata setting"
         if verbose:
             print(errStr)
         response = {"errorFlag": True, "errorString": errStr}
+
     return response
 
 
@@ -330,16 +350,9 @@ def GetStratigraphicLog(root, indexList=[], indexRange=(0, 0), verbose=False):
     else:
         siGroup = resp["value"]
         data = []
-        maxValidIndex = min(
-            siGroup.dimensions["index"].size, siGroup.getncattr("index_MaxValid")
-        )
+        maxValidIndex = min(siGroup.dimensions["index"].size, siGroup.getncattr("index_MaxValid"))
         # Select all option
-        if (
-            indexList == []
-            and len(indexRange) == 2
-            and indexRange[0] == 0
-            and indexRange[1] == 0
-        ):
+        if indexList == [] and len(indexRange) == 2 and indexRange[0] == 0 and indexRange[1] == 0:
             # Select all
             for i in range(0, maxValidIndex):
                 data.append((siGroup.variables.get("stratigraphicLayers")[i]))
@@ -351,11 +364,7 @@ def GetStratigraphicLog(root, indexList=[], indexRange=(0, 0), verbose=False):
                     data.append((siGroup.variables.get("stratigraphicLayers")[i]))
             response["value"] = data
         # Select based on indices range option
-        elif (
-            len(indexRange) == 2
-            and indexRange[0] >= 0
-            and indexRange[1] >= indexRange[0]
-        ):
+        elif len(indexRange) == 2 and indexRange[0] >= 0 and indexRange[1] >= indexRange[0]:
             for i in range(indexRange[0], indexRange[1]):
                 if int(i) >= 0 and int(i) < maxValidIndex:
                     data.append((siGroup.variables.get("stratigraphicLayers")[i]))
@@ -368,6 +377,91 @@ def GetStratigraphicLog(root, indexList=[], indexRange=(0, 0), verbose=False):
     return response
 
 
+def SetStratigraphicThicknesses(root, data, headers=None,ncols=None,append=False, verbose=False):
+    response = {"errorFlag": False}
+    resp = GetExtractedInformationGroup(root)
+    if resp["errorFlag"]:
+        # Create Extracted Information Group as it doesn't exist
+        eiGroup = root.createGroup("ExtractedInformation")
+    else:
+        eiGroup = resp["value"]
+
+    resp = GetStratigraphicThicknessGroup(root)
+    if resp["errorFlag"]:
+        stGroup = eiGroup.createGroup("StratigraphicThickness")
+        stGroup.setncattr("index_MaxValid", -1)
+        stGroup.createDimension("index", None)
+        stratigraphicThicknessType_t = stGroup.createCompoundType(
+            LoopProjectFile.stratigraphicThicknessType, "stratigraphicThickness"
+        )
+        stGroup.createVariable(
+            "stratigraphicThicknesses",
+            stratigraphicThicknessType_t,
+            ("index"),
+            zlib=True,
+            complevel=9,
+        )
+    else:
+        stGroup = resp["value"]
+
+    if stGroup:
+        stratigraphicThicknesses = stGroup.variables["stratigraphicThicknesses"]
+        if headers:
+            stGroup.setncattr("headers", headers)
+        if ncols:
+            stGroup.setncattr("ncols", ncols)
+        index = 0
+        if append:
+            index = stGroup.dimensions["index"].size
+        for i in data:
+            stratigraphicThicknesses[index] = i
+            index += 1
+        stGroup.setncattr("index_MaxValid", index)
+    else:
+        errStr = "(ERROR) Failed to create stratigraphic log group for strata setting"
+        if verbose:
+            print(errStr)
+        response = {"errorFlag": True, "errorString": errStr}
+
+    return response
+
+
+def GetStratigraphicThicknesses(root, indexList=[], indexRange=(0, 0), verbose=False):
+    response = {"errorFlag": False}
+    resp = GetStratigraphicThicknessGroup(root)
+    if resp["errorFlag"]:
+        response = resp
+    else:
+        siGroup = resp["value"]
+        data = []
+        maxValidIndex = min(siGroup.dimensions["index"].size, siGroup.getncattr("index_MaxValid"))
+        # Select all option
+        response['attributes'] = {a:siGroup.getncattr(a) for a in siGroup.ncattrs()}
+        if indexList == [] and len(indexRange) == 2 and indexRange[0] == 0 and indexRange[1] == 0:
+            # Select all
+            for i in range(0, maxValidIndex):
+                data.append((siGroup.variables.get("stratigraphicThicknesses")[i]))
+            response["value"] = data
+        # Select based on list of indices option
+        elif indexList != []:
+            for i in indexList:
+                if int(i) >= 0 and int(i) < maxValidIndex:
+                    data.append((siGroup.variables.get("stratigraphicThicknesses")[i]))
+            response["value"] = data
+        # Select based on indices range option
+        elif len(indexRange) == 2 and indexRange[0] >= 0 and indexRange[1] >= indexRange[0]:
+            for i in range(indexRange[0], indexRange[1]):
+                if int(i) >= 0 and int(i) < maxValidIndex:
+                    data.append((siGroup.variables.get("stratigraphicThicknesses")[i]))
+            response["value"] = data
+        else:
+            errStr = "Non-implemented filter option"
+            if verbose:
+                print(errStr)
+            response = {"errorFlag": True, "errorString": errStr}
+    return response
+
+
 # Set drillhole log
 def SetDrillholeLog(root, data, append=False, verbose=False):
     """