major change: use luarocks to manage project

4 files changed, 0 insertions, 362 deletions

diff --git a/nn/init.lua b/nn/init.lua
deleted file mode 100644
index 1bafa77..0000000
--- a/nn/init.lua
+++ /dev/null
@@ -1,3 +0,0 @@
-require 'nn.layer_repo'
-require 'nn.param_repo'
-require 'nn.layer_dag'
diff --git a/nn/layer_dag.lua b/nn/layer_dag.lua
deleted file mode 100644
index 8e30216..0000000
--- a/nn/layer_dag.lua
+++ /dev/null
@@ -1,249 +0,0 @@
-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/nn/layer_repo.lua b/nn/layer_repo.lua
deleted file mode 100644
index 602c37c..0000000
--- a/nn/layer_repo.lua
+++ /dev/null
@@ -1,34 +0,0 @@
-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/nn/param_repo.lua b/nn/param_repo.lua
deleted file mode 100644
index ab971ba..0000000
--- a/nn/param_repo.lua
+++ /dev/null
@@ -1,76 +0,0 @@
-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