Major refactor to be consistent with cogent core coding principles

decoder/softmax.go

@@ -80,7 +80,7 @@ func (sm *SoftMax) InitLayer(ncats int, layers []emer.Layer) {
 	sm.Layers = layers
 	nin := 0
 	for _, ly := range sm.Layers {
-		nin += ly.Shape().Len()
+		nin += ly.AsEmer().Shape.Len()
 	}
 	sm.Init(ncats, nin)
 }
@@ -143,12 +143,13 @@ func (sm *SoftMax) ValuesTsr(name string) *tensor.Float32 {
 func (sm *SoftMax) Input(varNm string, di int) {
 	off := 0
 	for _, ly := range sm.Layers {
-		tsr := sm.ValuesTsr(ly.Name())
-		ly.UnitValuesTensor(tsr, varNm, di)
+		lb := ly.AsEmer()
+		tsr := sm.ValuesTsr(lb.Name)
+		lb.UnitValuesTensor(tsr, varNm, di)
 		for j, v := range tsr.Values {
 			sm.Inputs[off+j] = v
 		}
-		off += ly.Shape().Len()
+		off += lb.Shape.Len()
 	}
 }
 

doc.go

@@ -23,11 +23,11 @@ and easier support for making permuted random lists, etc.
 
 * netview provides the NetView interactive 3D network viewer, implemented in the Cogent Core 3D framework.
 
-* path is a separate package for defining patterns of connectivity between layers
-(i.e., the ProjectionSpecs from C++ emergent).  This is done using a fully independent
-structure that *only* knows about the shapes of the two layers, and it returns a fully general
-bitmap representation of the pattern of connectivity between them.  The leabra.Path code
-then uses these patterns to do all the nitty-gritty of connecting up neurons.
+* path is a separate package for defining patterns of connectivity between layers.
+This is done using a fully independent structure that *only* knows about the shapes
+of the two layers, and it returns a fully general bitmap representation of the pattern
+of connectivity between them.  The leabra.Path code then uses these patterns to do
+all the nitty-gritty of connecting up neurons.
 This makes the pathway code *much* simpler compared to the ProjectionSpec in C++ emergent,
 which was involved in both creating the pattern and also all the complexity of setting up the
 actual connections themselves.  This should be the *last* time any of those pathway patterns

ecmd/std.go

@@ -46,7 +46,7 @@ func LogFilename(logName, netName, runName string) string {
 
 // ProcStd processes the standard args, after Parse has been called
 // for help, note, params, tag and wts
-func (ar *Args) ProcStd(params *emer.Params) {
+func (ar *Args) ProcStd(params *emer.NetParams) {
 	if ar.Bool("help") {
 		ar.Usage()
 		os.Exit(0)
@@ -55,8 +55,8 @@ func (ar *Args) ProcStd(params *emer.Params) {
 		mpi.Printf("note: %s\n", note)
 	}
 	if pars := ar.String("params"); pars != "" {
-		params.ExtraSets = pars
-		mpi.Printf("Using ParamSet: %s\n", params.ExtraSets)
+		// params.ExtraSets = pars // todo:
+		// mpi.Printf("Using ParamSet: %s\n", params.ExtraSets)
 	}
 	if tag := ar.String("tag"); tag != "" {
 		params.Tag = tag
@@ -71,7 +71,7 @@ func (ar *Args) ProcStd(params *emer.Params) {
 // setting the log files for standard log file names using netName
 // and params.RunName to identify the network / sim and run params, tag,
 // and starting run number
-func (ar *Args) ProcStdLogs(logs *elog.Logs, params *emer.Params, netName string) {
+func (ar *Args) ProcStdLogs(logs *elog.Logs, params *emer.NetParams, netName string) {
 	runName := params.RunName(ar.Int("run")) // used for naming logs, stats, etc
 	if ar.Bool("epclog") {
 		fnm := LogFilename("epc", netName, runName)

egui/netview.go

@@ -48,6 +48,6 @@ func (gui *GUI) SaveNetData(extra string) {
 	if gui.NetData == nil {
 		return
 	}
-	ndfn := gui.NetData.Net.Name() + "_" + extra + ".netdata.gz"
+	ndfn := gui.NetData.Net.AsEmer().Name + "_" + extra + ".netdata.gz"
 	gui.NetData.SaveJSON(core.Filename(ndfn))
 }

elog/context.go

@@ -8,6 +8,7 @@ import (
 	"fmt"
 	"log"
 
+	"cogentcore.org/core/base/errors"
 	"cogentcore.org/core/tensor"
 	"cogentcore.org/core/tensor/stats/metric"
 	"cogentcore.org/core/tensor/stats/stats"
@@ -233,27 +234,27 @@ func (ctx *Context) ItemColTensorScope(scope etime.ScopeKey, itemNm string) tens
 ///////////////////////////////////////////////////
 //  Network
 
-// Layer returns layer by name as the emer.Layer interface --
-// you may then need to convert to a concrete type depending.
+// Layer returns layer by name as the emer.Layer interface.
+// May then need to convert to a concrete type depending.
 func (ctx *Context) Layer(layNm string) emer.Layer {
-	return ctx.Net.LayerByName(layNm)
+	return errors.Log1(ctx.Net.AsEmer().EmerLayerByName(layNm))
 }
 
 // GetLayerTensor gets tensor of Unit values on a layer for given variable
 // from current ctx.Di data parallel index.
 func (ctx *Context) GetLayerTensor(layNm, unitVar string) *tensor.Float32 {
 	ly := ctx.Layer(layNm)
 	tsr := ctx.Stats.F32Tensor(layNm)
-	ly.UnitValuesTensor(tsr, unitVar, ctx.Di)
+	ly.AsEmer().UnitValuesTensor(tsr, unitVar, ctx.Di)
 	return tsr
 }
 
-// GetLayerRepTensor gets tensor of representative Unit values on a layer for given variable
+// GetLayerSampleTensor gets tensor of representative Unit values on a layer for given variable
 // from current ctx.Di data parallel index.
-func (ctx *Context) GetLayerRepTensor(layNm, unitVar string) *tensor.Float32 {
+func (ctx *Context) GetLayerSampleTensor(layNm, unitVar string) *tensor.Float32 {
 	ly := ctx.Layer(layNm)
 	tsr := ctx.Stats.F32Tensor(layNm)
-	ly.UnitValuesRepTensor(tsr, unitVar, ctx.Di)
+	ly.AsEmer().UnitValuesSampleTensor(tsr, unitVar, ctx.Di)
 	return tsr
 }
 
@@ -265,10 +266,10 @@ func (ctx *Context) SetLayerTensor(layNm, unitVar string) *tensor.Float32 {
 	return tsr
 }
 
-// SetLayerRepTensor sets tensor of representative Unit values on a layer for given variable
+// SetLayerSampleTensor sets tensor of representative Unit values on a layer for given variable
 // to current ctx.Di data parallel index.
-func (ctx *Context) SetLayerRepTensor(layNm, unitVar string) *tensor.Float32 {
-	tsr := ctx.GetLayerRepTensor(layNm, unitVar)
+func (ctx *Context) SetLayerSampleTensor(layNm, unitVar string) *tensor.Float32 {
+	tsr := ctx.GetLayerSampleTensor(layNm, unitVar)
 	ctx.SetTensor(tsr)
 	return tsr
 }

elog/stditems.go

@@ -9,6 +9,7 @@ import (
 	"reflect"
 	"time"
 
+	"cogentcore.org/core/base/errors"
 	"cogentcore.org/core/math32/minmax"
 	"cogentcore.org/core/tensor/stats/split"
 	"cogentcore.org/core/tensor/stats/stats"
@@ -292,26 +293,27 @@ func (lg *Logs) RunStats(stats ...string) {
 // to it so there aren't any duplicate items.
 // di is a data parallel index di, for networks capable of processing input patterns in parallel.
 func (lg *Logs) AddLayerTensorItems(net emer.Network, varNm string, mode etime.Modes, etm etime.Times, layClasses ...string) {
-	layers := net.LayersByClass(layClasses...)
+	en := net.AsEmer()
+	layers := en.LayersByClass(layClasses...)
 	for _, lnm := range layers {
 		clnm := lnm
-		cly := net.LayerByName(clnm)
+		cly := errors.Log1(en.EmerLayerByName(clnm))
 		itmNm := clnm + "_" + varNm
 		itm, has := lg.ItemByName(itmNm)
 		if has {
 			itm.Write[etime.Scope(mode, etm)] = func(ctx *Context) {
-				ctx.SetLayerRepTensor(clnm, varNm)
+				ctx.SetLayerSampleTensor(clnm, varNm)
 			}
 		} else {
 			lg.AddItem(&Item{
 				Name:      itmNm,
 				Type:      reflect.Float32,
-				CellShape: cly.RepShape().Sizes,
+				CellShape: cly.AsEmer().SampleShape.Sizes,
 				FixMin:    true,
 				Range:     minmax.F32{Max: 1},
 				Write: WriteMap{
 					etime.Scope(mode, etm): func(ctx *Context) {
-						ctx.SetLayerRepTensor(clnm, varNm)
+						ctx.SetLayerSampleTensor(clnm, varNm)
 					}}})
 		}
 	}

emer/README.md

@@ -1,15 +1,11 @@
 Docs: [GoDoc](https://pkg.go.dev/github.com/emer/emergent/v2/emer)
 
-Package emer provides minimal interfaces for the basic structural elements of neural networks
-including:
+Package emer provides minimal interfaces for the basic structural elements of neural networks including:
 * emer.Network, emer.Layer, emer.Unit, emer.Path (pathway that interconnects layers)
 
-These interfaces are intended to be just sufficient to support visualization and generic
-analysis kinds of functions, but explicitly avoid exposing ANY of the algorithmic aspects,
-so that those can be purely encoded in the implementation structs.
+These interfaces are intended to be just sufficient to support visualization and generic analysis kinds of functions, but explicitly avoid exposing ANY of the algorithmic aspects, so that those can be purely encoded in the implementation structs.
 
-At this point, given the extra complexity it would require, these interfaces do not support
-the ability to build or modify networks.
+At this point, given the extra complexity it would require, these interfaces do not support the ability to build or modify networks.
 
-Also added support for managing parameters in the `emer.Params` object, which handles standard parameter set logic and support for applying to networks, and the new `NetSize` map for configuring network size.
+Also added support for managing parameters in the `emer.Params` object, which handles standard parameter set logic and support for applying to networks, and the `NetSize` map for configuring network size.