Merge branch 'master' of https://gitlab.orr.noaa.gov/gnome/pygnome

.gitignore

@@ -23,7 +23,10 @@ py_gnome/build/**/*
 py_gnome/gnome.utilities.egg-info/*
 py_gnome/pyGnome.egg-info/*
 py_gnome/gnome/pyGnome.egg-info/*
+<<<<<<< Upstream, based on origin/develop
 py_gnome/documentation/_build/
+=======
+>>>>>>> 60dffaa replaced gitignore with develop ver
 
 # ignore sphinx built docs
 py_gnome/documentation/_build/

InstallingWithAnaconda.rst

@@ -115,7 +115,7 @@ Add the NOAA-ORR-ERD channel::
 
 Add the conda-forge channel::
 
-    > conda config --add channels conda forge
+    > conda config --add channels conda-forge
 
 When you add a channel to conda, it puts it at the top of the list. So now when you
 install a package, conda will first look in conda-forge, then NOAA-ORR-ERD, and

conda_requirements.txt

@@ -28,9 +28,8 @@ netCDF4=1.2.7
 awesome-slugify>=1.6
 regex>=2014.12
 unidecode>=0.04.19
-pyshp>=1.2
-pyugrid=0.2.3
-pysgrid=0.3.5
+pyshp=1.2.10
+gridded==0.0.9
 
 # NOAA maintained packages
 unit_conversion=2.5.5
@@ -42,7 +41,10 @@ cython=0.24.1
 
 # nice to have for development, not required to run
 pytest
+pytest-cov
+pytest-timeout
 testfixtures
+
 matplotlib
 sphinx
 sphinx_rtd_theme

experiments/property_experiments/test_grid_gen_scripts/circular.py

@@ -1,7 +1,5 @@
 import numpy as np
 
-from pysgrid import SGrid
-from gnome.environment.grid_property import GriddedProp
 
 import os
 from datetime import datetime, timedelta
@@ -20,12 +18,15 @@
 from gnome.movers.py_current_movers import PyCurrentMover
 
 from gnome.outputters import Renderer, NetCDFOutput
+
+from gnome.environment.gridded_objects_base import Grid_S, Variable
+
 x, y = np.mgrid[-30:30:61j, -30:30:61j]
 y = np.ascontiguousarray(y.T)
 x = np.ascontiguousarray(x.T)
 # y += np.sin(x) / 1
 # x += np.sin(x) / 5
-g = SGrid(node_lon=x,
+g = Grid_S(node_lon=x,
           node_lat=y)
 g.build_celltree()
 t = datetime(2000, 1, 1, 0, 0)
@@ -49,8 +50,8 @@
 # value[:,0] = x
 # value[:,1] = y
 
-vels_x = GriddedProp(name='v_x', units='m/s', time=[t], grid=g, data=vx)
-vels_y = GriddedProp(name='v_y', units='m/s', time=[t], grid=g, data=vy)
+vels_x = Variable(name='v_x', units='m/s', time=[t], grid=g, data=vx)
+vels_y = Variable(name='v_y', units='m/s', time=[t], grid=g, data=vy)
 vg = GridCurrent(variables=[vels_y, vels_x], time=[t], grid=g, units='m/s')
 point = np.zeros((1, 2))
 print vg.at(point, t)

gnome1/gui_gnome/CLASSES.CPP

@@ -594,7 +594,7 @@ short M51Click(DialogPtr dialog, short itemNum, long lParam, VOIDPTR data)
 			// should dispose if exists ?
 			gEditContourLevels = (DOUBLEH)_NewHandleClear(0);
 			// code goes here, should init fContourLevelsH if nil
-	 if((dynamic_cast<PtCurMap *>(gDialogTMap)) -> fContourLevelsH)
+	 		if((dynamic_cast<PtCurMap *>(gDialogTMap)) -> fContourLevelsH)
 			{
 				gEditContourLevels = (dynamic_cast<PtCurMap *>(gDialogTMap)) -> fContourLevelsH;
 				if(_HandToHand((Handle *)&gEditContourLevels))
@@ -656,21 +656,28 @@ OSErr M50Init(DialogPtr dialog, VOIDPTR data)
 
 	Float2EditText(dialog,M50REFLOATTIME, gDialogTMap -> fRefloatHalfLifeInHrs , 4);
 
-	SetButton (dialog, M25WANTEDCHANGEBOUNDS, dialogPtCurMap -> fUseBitMapBounds); // !EquaLWRect()
-
-	//SetButton (dialog, M25REPLACEMAP, false); 
-
-	wp.pLat = dialogPtCurMap -> fBitMapBounds.hiLat;
-	wp.pLong = dialogPtCurMap -> fBitMapBounds.loLong;
-	LL2EditTexts (dialog, M25TOPLATDEGREES, &wp);
+	if (gDialogTMap ->IAm(TYPE_MAP3D)) 	
+	{
+		SetButton (dialog, M25WANTEDCHANGEBOUNDS, false); // !EquaLWRect()
+		ShowHideBounds(dialog);	// for now using same enum values as M25 vector map dialog
+		ShowHideDialogItem(dialog,M25WANTEDCHANGEBOUNDS,false);
+		ShowHideDialogItem(dialog,M25FROST1,false);
+	}
+	else
+	{
+		SetButton (dialog, M25WANTEDCHANGEBOUNDS, dialogPtCurMap -> fUseBitMapBounds); // !EquaLWRect()
 
-	wp.pLat = dialogPtCurMap -> fBitMapBounds.loLat;
-	wp.pLong = dialogPtCurMap -> fBitMapBounds.hiLong;
-	LL2EditTexts (dialog, M25BOTTOMLATDEGREES, &wp);
+		wp.pLat = dialogPtCurMap -> fBitMapBounds.hiLat;
+		wp.pLong = dialogPtCurMap -> fBitMapBounds.loLong;
+		LL2EditTexts (dialog, M25TOPLATDEGREES, &wp);
 
-	//ShowHideBitMapBounds(dialog);
-	ShowHideBounds(dialog);	// for now using same enum values as M25 vector map dialog
+		wp.pLat = dialogPtCurMap -> fBitMapBounds.loLat;
+		wp.pLong = dialogPtCurMap -> fBitMapBounds.hiLong;
+		LL2EditTexts (dialog, M25BOTTOMLATDEGREES, &wp);
 
+		//ShowHideBitMapBounds(dialog);
+		ShowHideBounds(dialog);	// for now using same enum values as M25 vector map dialog
+	}
 	if (gDialogTMap ->IAm(TYPE_OSSMMAP)) 	// don't show refloat stuff since it varies with each grid cell
 	{
 		ShowHideDialogItem(dialog,M50REFLOATLABEL,false);
@@ -703,59 +710,67 @@ short M50Click(DialogPtr dialog, short itemNum, long lParam, VOIDPTR data)
 
 		case M50OK:
 			gDialogTMap -> fRefloatHalfLifeInHrs = EditText2Float(dialog,M50REFLOATTIME);
+
 			tempUseBounds = GetButton (dialog, M25WANTEDCHANGEBOUNDS);
 
-			if (tempUseBounds != dialogPtCurMap -> fUseBitMapBounds || tempUseBounds == true)
+			if (gDialogTMap ->IAm(TYPE_MAP3D)) 	
 			{
-				needToResetBitMap = true;
 			}
-
-			if(tempUseBounds)
+			else
 			{
-				long oneSecond = (1000000/3600);
-				// retrieve the extendedBounds
-				err = EditTexts2LL(dialog, M25TOPLATDEGREES, &p,TRUE);
-				if(err)break;
-				err = EditTexts2LL(dialog, M25BOTTOMLATDEGREES, &p2,TRUE);
-				if(err)break;
-
-				// get original map bounds for comparison
-				//origBounds = dialogTVectorMap -> fMapBounds;  // if use GetMapBounds() may return extended bounds
-				origBounds = gDialogTMap -> fMapBounds;  // if use GetMapBounds() may return extended bounds
-
-				// check extended bounds (oneSecond handles accuracy issue in reading from dialog)			
-				if (p.pLat > origBounds.hiLat + oneSecond || p2.pLat< origBounds.loLat - oneSecond
-					|| p.pLong < origBounds.loLong - oneSecond || p2.pLong > origBounds.hiLong + oneSecond)
+
+				if (tempUseBounds != dialogPtCurMap -> fUseBitMapBounds || tempUseBounds == true)
 				{
-					printError("The bitmap bounds must be less than the original bounds."); 
-					return 0; 
+					needToResetBitMap = true;
 				}
+
+				if(tempUseBounds)
+				{
+					long oneSecond = (1000000/3600);
+					// retrieve the extendedBounds
+					err = EditTexts2LL(dialog, M25TOPLATDEGREES, &p,TRUE);
+					if(err)break;
+					err = EditTexts2LL(dialog, M25BOTTOMLATDEGREES, &p2,TRUE);
+					if(err)break;
 
-				// just in case of round off
-				p.pLat = _min(p.pLat,origBounds.hiLat);
-				p.pLong = _max(p.pLong,origBounds.loLong);
-				p2.pLat = _max(p2.pLat,origBounds.loLat);
-				p2.pLong = _min(p2.pLong,origBounds.hiLong);
-			}
+					// get original map bounds for comparison
+					//origBounds = dialogTVectorMap -> fMapBounds;  // if use GetMapBounds() may return extended bounds
+					origBounds = gDialogTMap -> fMapBounds;  // if use GetMapBounds() may return extended bounds
+
+					// check extended bounds (oneSecond handles accuracy issue in reading from dialog)			
+					if (p.pLat > origBounds.hiLat + oneSecond || p2.pLat< origBounds.loLat - oneSecond
+						|| p.pLong < origBounds.loLong - oneSecond || p2.pLong > origBounds.hiLong + oneSecond)
+					{
+						printError("The bitmap bounds must be less than the original bounds."); 
+						return 0; 
+					}
+
+					// just in case of round off
+					p.pLat = _min(p.pLat,origBounds.hiLat);
+					p.pLong = _max(p.pLong,origBounds.loLong);
+					p2.pLat = _max(p2.pLat,origBounds.loLat);
+					p2.pLong = _min(p2.pLong,origBounds.hiLong);
+				}
 
-			dialogPtCurMap -> fUseBitMapBounds = GetButton (dialog, M25WANTEDCHANGEBOUNDS);
+				dialogPtCurMap -> fUseBitMapBounds = GetButton (dialog, M25WANTEDCHANGEBOUNDS);
 
-			if (dialogPtCurMap -> fUseBitMapBounds)
-			{
-				dialogPtCurMap -> fBitMapBounds.hiLat = p.pLat;
-				dialogPtCurMap -> fBitMapBounds.loLong = p.pLong;
-				dialogPtCurMap -> fBitMapBounds.loLat = p2.pLat;
-				dialogPtCurMap -> fBitMapBounds.hiLong = p2.pLong;
-				//err = dialogPtCurMap -> MakeBitmaps();
-				//if (!err) ChangeCurrentView(UnionWRect(settings.currentView, AddWRectBorders(dialogPtCurMap -> fBitMapBounds, 10)), TRUE, TRUE);
-			}
-			else
-				dialogPtCurMap -> fBitMapBounds = dialogPtCurMap -> GetMapBounds();			
+				if (dialogPtCurMap -> fUseBitMapBounds)
+				{
+					dialogPtCurMap -> fBitMapBounds.hiLat = p.pLat;
+					dialogPtCurMap -> fBitMapBounds.loLong = p.pLong;
+					dialogPtCurMap -> fBitMapBounds.loLat = p2.pLat;
+					dialogPtCurMap -> fBitMapBounds.hiLong = p2.pLong;
+					//err = dialogPtCurMap -> MakeBitmaps();
+					//if (!err) ChangeCurrentView(UnionWRect(settings.currentView, AddWRectBorders(dialogPtCurMap -> fBitMapBounds, 10)), TRUE, TRUE);
+				}
+				else
+					dialogPtCurMap -> fBitMapBounds = dialogPtCurMap -> GetMapBounds();			
 
-			if (needToResetBitMap) 
-			{
-				err = dialogPtCurMap -> MakeBitmaps();
-				if (!err) ChangeCurrentView(AddWRectBorders(dialogPtCurMap -> fBitMapBounds, 10), TRUE, TRUE);
+				if (needToResetBitMap) 
+				{
+					err = dialogPtCurMap -> MakeBitmaps();
+					if (!err) ChangeCurrentView(AddWRectBorders(dialogPtCurMap -> fBitMapBounds, 10), TRUE, TRUE);
+				}
 			}
 
 			return itemNum;

gnome1/gui_gnome/NetCDFWindMoverCurv.cpp

@@ -728,6 +728,9 @@ OSErr NetCDFWindMoverCurv::ReadTimeData(long index,VelocityFH *velocityH, char*
 				}
 				/*if (status != NC_NOERR)*//*err = -1; goto done;*/}}	// don't require
 		//if (status != NC_NOERR) {err = -1; goto done;}	// don't require
+		status = nc_get_att_float(ncid, wind_ucmp_id, "scale_factor", &scale_factor);
+		//if (status != NC_NOERR) {err = -1; goto done;}	// don't require scale factor
+
 	}	
 
 	status = nc_inq_attlen(ncid, wind_ucmp_id, "units", &velunit_len);
@@ -745,7 +748,6 @@ OSErr NetCDFWindMoverCurv::ReadTimeData(long index,VelocityFH *velocityH, char*
 		}
 	}
 
-
 	status = nc_close(ncid);
 	if (status != NC_NOERR) {err = -1; goto done;}
 
@@ -834,8 +836,9 @@ void NetCDFWindMoverCurv::Draw(Rect r, WorldRect view)
 	OSErr err = 0;
 	char errmsg[256];
 
-	RGBForeColor(&colors[PURPLE]);
-
+	//RGBForeColor(&colors[PURPLE]);
+	RGBForeColor(&fColor);
+
 	if(bShowArrows || bShowGrid)
 	{
 		if (bShowGrid) 	// make sure to draw grid even if don't draw arrows

gnome1/gui_gnome/TimeValuesIOPD.cpp

@@ -73,8 +73,15 @@ TOSSMTimeValue* CreateTOSSMTimeValue(TMover *theOwner,char* path, char* shortFil
 	else 
 	{
 #if TARGET_API_MAC_CARBON
-		err = ConvertTraditionalPathToUnixPath((const char *) path, outPath, kMaxNameLen) ;
-		if (!err) strcpy(path,outPath);
+		if(model && model->fWizard && model->fWizard->PathIsWizardResource(path))
+		{
+			// don't mess up the resource path
+		}
+		else 
+		{
+			err = ConvertTraditionalPathToUnixPath((const char *) path, outPath, kMaxNameLen) ;
+			if (!err) strcpy(path,outPath);
+		}
 #endif
 
 		if (IsTimeFile(path) || IsHydrologyFile(path) || IsOSSMTimeFile(path, &unitsIfKnownInAdvance))

lib_gnome/CurrentMover_c.cpp

@@ -162,7 +162,7 @@ OSErr CurrentMover_c::AllocateUncertainty(int numLESets, int* LESetsSizesList)	/
 
 	this->DisposeUncertainty(); // get rid of any old values
 
-	if (numLESets == 0) return -1;	// shouldn't happen - if we get here there should be an uncertainty set
+	//if (numLESets == 0) return -1;	// shouldn't happen - if we get here there should be an uncertainty set - unless there is no spill...
 
 	if(!(fLESetSizesH = (LONGH)_NewHandle(sizeof(long)*numLESets)))goto errHandler;
 

lib_gnome/GridCurrentMover_c.cpp

@@ -541,7 +541,14 @@ OSErr GridCurrentMover_c::GetScaledVelocities(Seconds model_time, VelocityFRec *
 
 LongPointHdl GridCurrentMover_c::GetPointsHdl(void)
 {
-	return timeGrid->fGrid->GetPointsHdl();
+	if (timeGrid->IsRegularGrid())
+	{
+		return timeGrid->GetPointsHdl();
+	}
+	else
+	{
+		return timeGrid->fGrid->GetPointsHdl();
+	}
 }
 
 TopologyHdl GridCurrentMover_c::GetTopologyHdl(void)
@@ -557,7 +564,12 @@ GridCellInfoHdl GridCurrentMover_c::GetCellDataHdl(void)
 WORLDPOINTH	GridCurrentMover_c::GetTriangleCenters(void)
 {	// should rename this function...
 	if (IsTriangleGrid())
-		return timeGrid->fGrid->GetCenterPointsHdl();
+	{
+		if (IsDataOnCells())
+			return timeGrid->fGrid->GetCenterPointsHdl();
+		else
+			return timeGrid->fGrid->GetWorldPointsHdl();
+	}
 	else
 		return timeGrid->GetCellCenters();
 }

lib_gnome/GridCurrentMover_c.h

@@ -81,6 +81,7 @@ class DLL_API GridCurrentMover_c : virtual public CurrentMover_c {
 			long 		GetNumPoints(void);
 			bool 		IsTriangleGrid(){return timeGrid->IsTriangleGrid();}
 			bool 		IsDataOnCells(){return timeGrid->IsDataOnCells();}
+			bool 		IsRegularGrid(){return timeGrid->IsRegularGrid();}
 
 			OSErr		get_move(int n, Seconds model_time, Seconds step_len, WorldPoint3D* ref, WorldPoint3D* delta, short* LE_status, LEType spillType, long spill_ID);
 

lib_gnome/GridVel_c.h

@@ -49,6 +49,7 @@ class GridVel_c {
 	virtual InterpolationValBilinear GetBilinearInterpolationValues(WorldPoint ref){InterpolationValBilinear ival; memset(&ival,0,sizeof(ival)); return ival;}
 	virtual InterpolationVal GetInterpolationValues(WorldPoint ref){InterpolationVal ival; memset(&ival,0,sizeof(ival)); return ival;}
 	virtual LongPointHdl GetPointsHdl(void){return 0;}
+	virtual WORLDPOINTH GetWorldPointsHdl(void){return 0;}
 	virtual TopologyHdl GetTopologyHdl(void){return 0;}
 	virtual WORLDPOINTH	GetCenterPointsHdl(void){return 0;}
 	virtual double GetDepthAtPoint(WorldPoint p){return 0;}

lib_gnome/OSSMTimeValue_c.cpp

@@ -735,7 +735,7 @@ OSErr OSSMTimeValue_c::ReadNDBCWind(vector<string> &linesInFile, long numHeaderL
 		if (lineStream.fail()) {
 			// scan will allow comment at end of line, for now just ignore
 			err = -1;
-			TechError("OSSMTimeValue_c::ReadTimeValues()", "scan data values", 0);
+			TechError("OSSMTimeValue_c::ReadNDBCWind()", "scan data values", 0);
 			goto done;
 		}
 
@@ -847,13 +847,28 @@ OSErr OSSMTimeValue_c::ReadTimeValues(char *path, short format, short unitsIfKno
 	//strcpy(this->fileName, path); // for now use full path
 //#endif
 
+#ifndef pyGNOME
+	// location files need special case code that is in ReadFileContents
+	CHARH f = 0;
+	if ((err = ReadFileContents(TERMINATED,0, 0, path, 0, 0, &f)) != 0) {
+		TechError("TOSSMTimeValue::ReadTimeValues()", "ReadFileContents()", 0);
+		return -1;
+	}
 	vector<string> linesInFile;
-	if (ReadLinesInFile(path, linesInFile)) {
+	if (ReadLinesInBuffer(f, linesInFile)) {
 		linesInFile = rtrim_empty_lines(linesInFile);
 	}
 	else
 		return -1; // we failed to read in the file.
 
+#else	
+	vector<string> linesInFile;
+	if (ReadLinesInFile(path, linesInFile)) {
+		linesInFile = rtrim_empty_lines(linesInFile);
+	}
+	else
+		return -1; // we failed to read in the file.
+#endif
 	numLines = linesInFile.size();
 
 	if (IsNDBCWindFile(linesInFile, &numHeaderLines)) {