major change: use luarocks to manage project

4 files changed, 362 insertions, 0 deletions

diff --git a/nerv/nn/init.lua b/nerv/nn/init.lua
new file mode 100644
index 0000000..cbaf52b
--- /dev/null
+++ b/nerv/nn/init.lua
@@ -0,0 +1,3 @@
+nerv.include('layer_repo.lua')
+nerv.include('param_repo.lua')
+nerv.include('layer_dag.lua')
diff --git a/nerv/nn/layer_dag.lua b/nerv/nn/layer_dag.lua
new file mode 100644
index 0000000..8e30216
--- /dev/null
+++ b/nerv/nn/layer_dag.lua
@@ -0,0 +1,249 @@
+local DAGLayer = nerv.class("nerv.DAGLayer", "nerv.Layer")
+
+local function parse_id(str)
+    local id, port, _
+    _, _, id, port = string.find(str, "([a-zA-Z0-9_]+)%[([0-9]+)%]")
+    if id == nil or port == nil then
+        _, _, id, port = string.find(str, "(.+)%[([0-9]+)%]")
+        if not (id == "<input>" or id == "<output>") then
+            nerv.error("wrong format of connection id")
+        end
+    end
+    port = tonumber(port)
+    return id, port
+end
+
+local function discover(id, layers, layer_repo)
+    local ref = layers[id]
+    if id == "<input>" or id == "<output>" then
+        return nil
+    end
+    if ref == nil then
+        local layer = layer_repo:get_layer(id)
+        local dim_in, dim_out = layer:get_dim()
+        ref = {
+            layer = layer,
+            inputs = {},
+            outputs = {},
+            err_inputs = {},
+            err_outputs = {},
+            next_layers = {},
+            input_len = #dim_in,
+            output_len = #dim_out,
+            in_deg = 0,
+            visited = false
+        }
+        layers[id] = ref
+    end
+    return ref
+end
+
+function DAGLayer:__init(id, global_conf, layer_conf)
+    local layers = {}
+    local inputs = {}
+    local outputs = {}
+    local dim_in = layer_conf.dim_in
+    local dim_out = layer_conf.dim_out
+    local parsed_conn = {}
+    for from, to in pairs(layer_conf.connections) do
+        local id_from, port_from = parse_id(from)
+        local id_to, port_to = parse_id(to)
+        local ref_from = discover(id_from, layers, layer_conf.sub_layers)
+        local ref_to = discover(id_to, layers, layer_conf.sub_layers)
+        local input_dim, output_dim, _
+        if ref_from and ref_from.outputs[port_from] ~= nil then
+            nerv.error("%s has already been attached", from)
+        end
+        if ref_to and ref_to.inputs[port_to] ~= nil then
+            nerv.error("%s has already been attached", to)
+        end
+        if id_from == "<input>" then
+            input_dim, _ = ref_to.layer:get_dim()
+            if dim_in[port_from] ~= input_dim[port_to] then
+                nerv.error("mismatching data dimension between %s and %s", from, to)
+            end
+            inputs[port_from] = {ref_to, port_to}
+            ref_to.inputs[port_to] = inputs -- just a place holder
+        elseif id_to == "<output>" then
+            _, output_dim = ref_from.layer:get_dim()
+            if output_dim[port_from] ~= dim_out[port_to] then
+                nerv.error("mismatching data dimension between %s and %s", from, to)
+            end
+            outputs[port_to] = {ref_from, port_from}
+            ref_from.outputs[port_from] = outputs -- just a place holder
+        else
+            _, output_dim = ref_from.layer:get_dim()
+            input_dim, _ = ref_to.layer:get_dim()
+            if output_dim[port_from] ~= input_dim[port_to] then
+                nerv.error("mismatching data dimension between %s and %s", from, to)
+            end
+
+            table.insert(parsed_conn,
+                {{ref_from, port_from}, {ref_to, port_to}})
+            table.insert(ref_from.next_layers, ref_to) -- add edge
+            ref_to.in_deg = ref_to.in_deg + 1          -- increase the in-degree of the target layer
+        end
+    end
+
+    -- topology sort
+    local queue = {}
+    local l = 1
+    local r = 1
+    for id, ref in pairs(layers) do
+        if ref.in_deg == 0 then
+            table.insert(queue, ref)
+            nerv.info("adding source layer: %s", id)
+            r = r + 1
+        end
+    end
+    if l == r then
+        nerv.error("loop detected")
+    end
+    while l < r do
+        local cur = queue[l]
+        cur.visited = true
+        l = l + 1
+        for _, nl in pairs(cur.next_layers) do
+            nl.in_deg = nl.in_deg - 1 
+            if nl.in_deg == 0 then
+                table.insert(queue, nl)
+                r = r + 1
+            end
+        end
+    end
+    for i = 1, #queue do
+        nerv.info("enqueued layer: %s", queue[i].layer.id)
+    end
+
+    for id, ref in pairs(layers) do
+        -- check wether the graph is connected
+        if ref.visited == false then
+            nerv.warning("layer %s is ignored", id)
+        end
+    end
+
+    self.layers = layers
+    self.inputs = inputs
+    self.outputs = outputs
+    self.dim_in = dim_in
+    self.dim_out = dim_out
+    self.parsed_conn = parsed_conn
+    self.queue = queue
+    self.gconf = global_conf
+end
+
+function DAGLayer:init(batch_size)
+    for i, conn in ipairs(self.parsed_conn) do
+        local _, output_dim
+        local ref_from, port_from, ref_to, port_to
+        ref_from, port_from = unpack(conn[1])
+        ref_to, port_to = unpack(conn[2])
+        _, output_dim = ref_from.layer:get_dim()
+        local mid = self.gconf.cumat_type(batch_size,
+                                        output_dim[port_from])
+        local err_mid = mid:create()
+
+        ref_from.outputs[port_from] = mid
+        ref_to.inputs[port_to] = mid
+
+        ref_from.err_inputs[port_from] = err_mid
+        ref_to.err_outputs[port_to] = err_mid
+    end
+    for id, ref in pairs(self.layers) do
+        for i = 1, ref.input_len do
+            if ref.inputs[i] == nil then
+                nerv.error("dangling input port %d of layer %s", i, id)
+            end
+        end
+        for i = 1, ref.output_len do
+            if ref.outputs[i] == nil then
+                nerv.error("dangling output port %d of layer %s", i, id)
+            end
+        end
+        -- initialize sub layers
+        ref.layer:init(batch_size)
+    end
+    for i = 1, #self.dim_in do
+        if self.inputs[i] == nil then
+            nerv.error("dangling port %d of layer <input>", i)
+        end
+    end
+    for i = 1, #self.dim_out do
+        if self.outputs[i] == nil then
+            nerv.error("dangling port %d of layer <output>", i)
+        end
+    end
+end
+
+function DAGLayer:set_inputs(input)
+    for i = 1, #self.dim_in do
+        local layer = self.inputs[i][1]
+        local port = self.inputs[i][2]
+        layer.inputs[port] = input[i]
+    end
+end
+
+function DAGLayer:set_outputs(output)
+    for i = 1, #self.dim_out do
+        local layer = self.outputs[i][1]
+        local port = self.outputs[i][2]
+        layer.outputs[port] = output[i]
+    end
+end
+
+function DAGLayer:set_err_inputs(bp_err)
+    for i = 1, #self.dim_out do
+        local layer = self.outputs[i][1]
+        local port = self.outputs[i][2]
+        layer.err_inputs[port] = bp_err[i]
+    end
+end
+
+function DAGLayer:set_err_outputs(next_bp_err)
+    for i = 1, #self.dim_in do
+        local layer = self.inputs[i][1]
+        local port = self.inputs[i][2]
+        layer.err_outputs[port] = next_bp_err[i]
+    end
+end
+
+function DAGLayer:update(bp_err, input, output)
+    self:set_err_inputs(bp_err)
+    self:set_inputs(input)
+    self:set_outputs(output)
+    -- print("update")
+    for id, ref in pairs(self.queue) do
+        -- print(ref.layer.id)
+        ref.layer:update(ref.err_inputs, ref.inputs, ref.outputs)
+    end
+end
+
+function DAGLayer:propagate(input, output)
+    self:set_inputs(input)
+    self:set_outputs(output)
+    for i = 1, #self.queue do
+        local ref = self.queue[i]
+        -- print(ref.layer.id)
+        ref.layer:propagate(ref.inputs, ref.outputs)
+    end
+end
+
+function DAGLayer:back_propagate(bp_err, next_bp_err, input, output)
+    self:set_err_outputs(next_bp_err)
+    self:set_err_inputs(bp_err)
+    self:set_inputs(input)
+    self:set_outputs(output)
+    for i = #self.queue, 1, -1 do
+        local ref = self.queue[i]
+        -- print(ref.layer.id)
+        ref.layer:back_propagate(ref.err_inputs, ref.err_outputs, ref.inputs, ref.outputs)
+    end
+end
+
+function DAGLayer:get_params()
+    local param_repos = {}
+    for id, ref in pairs(self.queue) do
+        table.insert(param_repos, ref.layer:get_params())
+    end
+    return nerv.ParamRepo.merge(param_repos)
+end
diff --git a/nerv/nn/layer_repo.lua b/nerv/nn/layer_repo.lua
new file mode 100644
index 0000000..602c37c
--- /dev/null
+++ b/nerv/nn/layer_repo.lua
@@ -0,0 +1,34 @@
+local LayerRepo = nerv.class("nerv.LayerRepo")
+
+function LayerRepo:__init(layer_spec, param_repo, global_conf)
+    local layers = {}
+    for ltype, llist in pairs(layer_spec) do
+        local layer_type = nerv.get_type(ltype)
+        for id, spec in pairs(llist) do
+            if layers[id] ~= nil then
+                nerv.error("a layer with id %s already exists", id)
+            end
+            nerv.info("create layer: %s", id)
+            if type(spec[2]) ~= "table" then
+                nerv.error("layer config table is need")
+            end
+            layer_config = spec[2]
+            if type(spec[1]) ~= "table" then
+                nerv.error("parameter description table is needed")
+            end
+            for pname, pid in pairs(spec[1]) do
+                layer_config[pname] = param_repo:get_param(pid)
+            end
+            layers[id] = layer_type(id, global_conf, layer_config)
+        end
+    end
+    self.layers = layers
+end
+
+function LayerRepo:get_layer(lid)
+    local layer = self.layers[lid]
+    if layer == nil then
+        nerv.error("layer with id %s not found", lid)
+    end
+    return layer
+end
diff --git a/nerv/nn/param_repo.lua b/nerv/nn/param_repo.lua
new file mode 100644
index 0000000..ab971ba
--- /dev/null
+++ b/nerv/nn/param_repo.lua
@@ -0,0 +1,76 @@
+local ParamRepo = nerv.class("nerv.ParamRepo")
+function ParamRepo:__init(plist)
+    self.params = {}
+    if plist ~= nil then
+        for i, p in ipairs(plist) do
+            self.params[p.id] = p
+        end
+    end
+end
+
+function ParamRepo:add(pid, p)
+    if self.params[pid] ~= nil then
+        nerv.error("duplicate params with the same id: %s", pid)
+    end
+    self.params[pid] = p
+end
+
+function ParamRepo:remove(pid, p)
+    if self.params[pid] == nil then
+        nerv.error("param %s does not exit", pid)
+    end
+    table.remove(self.params, pid)
+end
+
+function ParamRepo.merge(repos)
+    local self = nerv.ParamRepo()
+    for i, repo in ipairs(repos) do
+        if not nerv.is_type(repo, "nerv.ParamRepo") then
+            nerv.error("nerv.ParamRepo objects expected, got %s", repo)
+        end
+        for pid, p in pairs(repo.params) do
+            self:add(pid, p)
+        end
+    end
+    return self
+end
+
+function ParamRepo:import(param_files, pids, gconf)
+    if type(param_files) ~= "table" then
+        nerv.error("param file table is need")
+    end
+    for i = 1, #param_files do
+        local pf = nerv.ChunkFile(param_files[i], "r")
+        for cid, cspec in pairs(pf.metadata) do
+            if pids == nil or pids[cid] ~= nil then
+                local p = pf:read_chunk(cid, gconf)
+                if not nerv.is_type(p, "nerv.Param") then
+                    nerv.error("param chunk is expected")
+                end
+                self:add(cid, p)
+            end
+        end
+    end
+end
+
+function ParamRepo:export(param_file, pids)
+    cf = nerv.ChunkFile(param_file, "w")
+    if pids == nil then
+        for id, p in pairs(self.params) do
+            cf:write_chunk(p)
+        end
+    else
+        for i, pid in ipairs(pids) do
+            cf:write_chunk(self:get_param(pid))
+        end
+    end
+    cf:close()
+end
+
+function ParamRepo:get_param(pid)
+    local p = self.params[pid]
+    if p == nil then
+        nerv.error("param with id %s not found", pid)
+    end
+    return p
+end