Merge branch 'master' into pythonic

Author: lachlangrose

.github/workflows/publish_conda.yml

@@ -27,7 +27,7 @@ jobs:
           ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN  }}
         shell: bash -l {0}
         run: |
-           conda install -c conda-forge conda-build netCDF4 numpy anaconda-client -y
+           conda install -c conda-forge conda-build netCDF4>=1.5.4 numpy anaconda-client -y
            conda build -c anaconda -c conda-forge -c loop3d --output-folder conda conda
            conda install anaconda-client -y
       - name: upload windows

LoopProjectFile/DataCollection.py

@@ -5,7 +5,7 @@
 # Check Data Collection valid if present
 def CheckDataCollectionValid(rootGroup, verbose=False):
     """
-    **CheckDataCollectionValid** - Checks for valid data collection group data 
+    **CheckDataCollectionValid** - Checks for valid data collection group data
     given a netCDF root node
 
     Parameters
@@ -18,7 +18,7 @@ def CheckDataCollectionValid(rootGroup, verbose=False):
     Returns
     -------
     bool
-        True if valid data collection formatting in project file, False 
+        True if valid data collection formatting in project file, False
         otherwise.
 
     """
@@ -53,6 +53,15 @@ def GetContactsGroup(rootGroup,verbose=False):
     else:
         return LoopProjectFileUtils.GetGroup(resp["value"],"Contacts",verbose)
 
+# Get Drillhole group if present
+def GetDrillholesGroup(rootGroup,verbose=False):
+    response = {"errorFlag":False}
+    resp = GetDataCollectionGroup(rootGroup,verbose)
+    if resp["errorFlag"]:
+        return resp
+    else:
+        return LoopProjectFileUtils.GetGroup(resp["value"],"Drillholes",verbose)
+
 def CreateObservationGroup(dataCollectionGroup):
     obGroup = dataCollectionGroup.createGroup("Observations")
     obGroup.createDimension("faultObservationIndex",None)
@@ -238,11 +247,12 @@ def SetContacts(root, data, append=False, verbose=False):
     else:
         dcGroup = resp["value"]
 
+    # Note contacts use a different group node "Contacts" hence we cannot use SetObservations function
     resp = GetContactsGroup(root)
     if resp["errorFlag"]:
         group = dcGroup.createGroup("Contacts")
         group.createDimension("index",None)
-        contactObservationType_t = group.createCompoundType(LoopProjectFile.contactObservationType,'contactObservationType')
+        contactObservationType_t = group.createCompoundType(LoopProjectFile.contactObservationType,'contactObservation')
         group.createVariable('contacts',contactObservationType_t,('index'),zlib=True,complevel=9)
     else:
         group = resp["value"]
@@ -260,9 +270,65 @@ def SetContacts(root, data, append=False, verbose=False):
         response = {"errorFlag":True,"errorString":errStr}
     return response
 
-#Extract contacts 
+# Set drillhole observations
+def SetDrillholeObservations(root, data, append=False, verbose=False):
+    """
+    **SetDrillholeObservations** - Saves a list of drillhole observaions in ((easting,northing,
+    altitude),(easting,northing,altitude),formation,dip,dipDir) format into the netCDF Loop Project File
+
+    Parameters
+    ----------
+    rootGroup: netCDF4.Group
+        The root group node of a Loop Project File
+    data: list of ((X,Y,Z),(X,Y,Z),formation,dip,dipDir)
+        The data to save
+    index: int
+        The index of this data
+    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
+        True
+
+    """
+    response = {"errorFlag":False}
+    resp = GetDataCollectionGroup(root)
+    if resp["errorFlag"]:
+        # Create Structural Models Group and add data shape based on project extents
+        dcGroup = root.createGroup("DataCollection")
+    else:
+        dcGroup = resp["value"]
+
+    # Note drillholes use a different group node "Drillholes" hence we cannot use SetObservations function
+    resp = GetDrillholesGroup(root)
+    if resp["errorFlag"]:
+        group = dcGroup.createGroup("Drillholes")
+        group.createDimension("index",None)
+        drillholeObservationType_t = group.createCompoundType(LoopProjectFile.drillholeObservationType,'drillholeObservation')
+        group.createVariable('drillholeObservations',drillholeObservationType_t,('index'),zlib=True,complevel=9)
+    else:
+        group = resp["value"]
+
+    if group:
+        drillholeObservationsLocation = group.variables['drillholeObservations']
+        if append: index = group.dimensions['index'].size
+        else: index = 0
+        for i in data:
+            drillholeObservationsLocation[index] = i
+            index += 1
+    else:
+        errStr = "(ERROR) Failed to Create contacts group for contact setting"
+        if verbose: print(errStr)
+        response = {"errorFlag":True,"errorString":errStr}
+    return response
+
+#Extract contacts
 def GetContacts(root, indexList=[], indexRange=(0,0), keyword="", verbose=False):
     response = {"errorFlag":False}
+    # Note contacts use a different group node "Contacts" hence we cannot use GetObservations function
     resp = GetContactsGroup(root)
     if resp["errorFlag"]: response = resp
     else:
@@ -307,6 +373,53 @@ def GetContacts(root, indexList=[], indexRange=(0,0), keyword="", verbose=False)
             response = {"errorFlag":True,"errorString":errStr}
     return response
 
+#Extract drillhole observaions
+def GetDrillholeObservations(root, indexList=[], indexRange=(0,0), keyword="", verbose=False):
+    response = {"errorFlag":False}
+    # Note contacts use a different group node "Contacts" hence we cannot use GetObservations function
+    resp = GetDrillholesGroup(root)
+    if resp["errorFlag"]: response = resp
+    else:
+        group = resp["value"]
+        data = []
+        # Select all option
+        if indexList==[] and len(indexRange) == 2 and indexRange[0] == 0 \
+          and indexRange[1] == 0 and keyword == "":
+            # Create list of observations as:
+            # ((easting,northing,altitude),dipdir,dip,formation,layer)
+            for i in range(0,group.dimensions['index'].size):
+                data.append((group.variables.get('drillholeObservations')[i]))
+            response["value"] = data
+        # Select based on keyword and list of indices option
+        elif keyword != "" and indexList != []:
+            for i in indexList:
+                if int(i) >= 0 and int(i) < group.dimensions['index'].size \
+                    and group.variables.get('layer')[i] == keyword:
+                    data.append((group.variables.get('drillholeObservations')[i]))
+            response["value"] = data
+        # Select based on keyword option
+        elif keyword != "":
+            for i in range(0,group.dimensions['index'].size):
+                if group.variables.get('layer')[i] == keyword:
+                    data.append((group.variables.get('drillholeObservations')[i]))
+            response["value"] = data
+        # Select based on list of indices option
+        elif indexList != []:
+            for i in indexList:
+                if int(i) >= 0 and int(i) < group.dimensions['index'].size:
+                    data.append((group.variables.get('drillholeObservations')[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) < group.dimensions['index'].size:
+                    data.append((group.variables.get('drillholeObservations')[i]))
+            response["value"] = data
+        else:
+            errStr = "Non-implemented filter option"
+            if verbose: print(errStr)
+            response = {"errorFlag":True,"errorString":errStr}
+    return response
 
 #Set data collection (map2loop) configuration settings
 def SetConfiguration(root, data, verbose=False):

LoopProjectFile/ExtractedInformation.py

@@ -42,6 +42,14 @@ def GetStratigraphicInformationGroup(rootGroup,verbose=False):
     else:
         return LoopProjectFileUtils.GetGroup(resp["value"],"StratigraphicInformation",verbose)
 
+def GetDrillholeDescriptionGroup(rootGroup,verbose=False):
+    response = {"errorFlag":False}
+    resp = GetExtractedInformationGroup(rootGroup,verbose)
+    if resp["errorFlag"]:
+        return resp
+    else:
+        return LoopProjectFileUtils.GetGroup(resp["value"],"DrillholeInformation",verbose)
+
 def GetEventLogGroup(rootGroup,verbose=False):
     response = {"errorFlag":False}
     resp = GetExtractedInformationGroup(rootGroup,verbose)
@@ -246,6 +254,91 @@ def GetStratigraphicLog(root, indexList=[], indexRange=(0,0), verbose=False):
             response = {"errorFlag":True,"errorString":errStr}
     return response
 
+# Set drillhole log
+def SetDrillholeLog(root, data, append=False, verbose=False):
+    """
+    **SetDrillholeLog** - Saves a list of drillholes in (collarId, name,
+    location(X,Y,Z)) format into the netCDF Loop Project File
+
+    Parameters
+    ----------
+    rootGroup: netCDF4.Group
+        The root group node of a Loop Project File
+    data: list of (collarId, name, location)
+        The data to save
+    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
+        True
+
+    """
+    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 = GetStratigraphicInformationGroup(root)
+    if resp["errorFlag"]:
+        siGroup = eiGroup.createGroup("DrillholeInformation")
+        siGroup.createDimension("index",None)
+        drillholeDescriptionType_t = siGroup.createCompoundType(LoopProjectFile.drillholeDescriptionType,'DrillholeDescription')
+        siGroup.createVariable('drillholeDescriptions',drillholeDescriptionType_t,('index'),zlib=True,complevel=9)
+    else:
+        siGroup = resp["value"]
+
+    if siGroup:
+        drillholeDescriptionsLocation = siGroup.variables['drillholeDescriptions']
+        index = 0
+        if append: index = siGroup.dimensions['index'].size
+        for i in data:
+            drillholeDescriptionsLocation[index] = i
+            index += 1
+    else:
+        errStr = "(ERROR) Failed to create drillhole description log group for setting drillhole data"
+        if verbose: print(errStr)
+        response = {"errorFlag":True,"errorString":errStr}
+    return response
+
+def GetDrillholeLog(root, indexList=[], indexRange=(0,0), verbose=False):
+    response = {"errorFlag":False}
+    resp = GetDrillholeDescriptionGroup(root)
+    if resp["errorFlag"]: response = resp
+    else:
+        siGroup = resp["value"]
+        data = []
+        # Select all option
+        if indexList==[] and len(indexRange) == 2 and indexRange[0] == 0 \
+          and indexRange[1] == 0:
+            # Select all
+            for i in range(0,siGroup.dimensions['index'].size):
+                data.append((siGroup.variables.get('drillholeDescriptions')[i]))
+            response["value"] = data
+        # Select based on list of indices option
+        elif indexList != []:
+            for i in indexList:
+                if int(i) >= 0 and int(i) < siGroup.dimensions['index'].size:
+                    data.append((siGroup.variables.get('drillholeDescriptions')[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) < siGroup.dimensions['index'].size:
+                    data.append((siGroup.variables.get('drillholeDescriptions')[i]))
+            response["value"] = data
+        else:
+            errStr = "Non-implemented filter option"
+            if verbose: print(errStr)
+            response = {"errorFlag":True,"errorString":errStr}
+    return response
 
 def SetEventRelationships(root, data, append=False, verbose=False):
     response = {"errorFlag":False}