local TNN = nerv.class("nerv.TNN")

local function parse_id(str)
    --used to parse layerid[portid],time
    local id, port, time, _
    _, _, id, port, time = string.find(str, "([a-zA-Z0-9_]+)%[([0-9]+)%][,]*([0-9]*)")
    if id == nil or port == nil then
        _, _, id, port, time = string.find(str, "(.+)%[([0-9]+)%][,]*([0-9]*)")
        if not (id == "<input>" or id == "<output>") then
            nerv.error("wrong format of connection id")
        end
    end
    --print(str, id, port, time)
    port = tonumber(port)
    if (time == nil) then
        time = 0
    else
        time = tonumber(time)
    end
    --now time don't need to be parsed
    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,
            id = layer.id,
            inputs_m = {}, --storage for computation, inputs_m[time][port]
            inputs_b = {}, --inputs_g[time][port], whether this input can been computed
            inputs_matbak_p = {}, --which is a back-up space to handle some cross-border computation, inputs_p_matbak[port]
            outputs_m = {},
            outputs_b = {},
            err_inputs_m = {},
            err_inputs_matbak_p = {}, --which is a back-up space to handle some cross-border computation
            err_inputs_b = {},
            err_outputs_m = {},
            err_outputs_b = {},
            i_conns_p = {}, --list of inputing connections
            o_conns_p = {}, --list of outputing connections
            dim_in = dim_in, --list of dimensions of ports
            dim_out = dim_out,
        }
        layers[id] = ref
    end
    return ref
end

nerv.TNN.FC = {} --flag const
nerv.TNN.FC.SEQ_START = 4
nerv.TNN.FC.SEQ_END = 8 
nerv.TNN.FC.HAS_INPUT = 1
nerv.TNN.FC.HAS_LABEL = 2
nerv.TNN.FC.SEQ_NORM = bit.bor(nerv.TNN.FC.HAS_INPUT, nerv.TNN.FC.HAS_LABEL) --This instance have both input and label

function TNN.make_initial_store(st, p, dim, batch_size, chunk_size, extend_t, global_conf, st_c, p_c, t_c)
    --Return a table of matrix storage from time (1-extend_t)..(chunk_size+extend_t)
    if (type(st) ~= "table") then
        nerv.error("st should be a table")
    end
    for i = 1 - extend_t - 2, chunk_size + extend_t + 2 do --intentionally allocated more time
        if (st[i] == nil) then
            st[i] = {}
        end
        st[i][p] = global_conf.cumat_type(batch_size, dim)
        st[i][p]:fill(0)
        if (st_c ~= nil) then
            if (st_c[i + t_c] == nil) then
                st_c[i + t_c] = {}
            end
            st_c[i + t_c][p_c] = st[i][p]
        end
    end
    collectgarbage("collect") --free the old one to save memory
end

function TNN:out_of_feedrange(t) --out of chunk, or no input, for the current feed
    if (t < 1 or t > self.chunk_size) then
        return true
    end
    if (self.feeds_now.flagsPack_now[t] == 0 or self.feeds_now.flagsPack_now[t] == nil) then
        return true
    end
    return false
end

function TNN:__init(id, global_conf, layer_conf)
    self.clip_t = layer_conf.clip_t
    if self.clip_t == nil then
        self.clip_t = 0
    end
    if self.clip_t > 0 then
        nerv.info("tnn(%s) will clip gradient across time with %f...", id, self.clip_t)
    end

    self.extend_t = layer_conf.extend_t --TNN will allocate storage of time for 1-extend_t .. chunk_size+extend_t
    if self.extend_t == nil then
        self.extend_t = 5 
    end
    nerv.info("tnn(%s) will extend storage beyond MB border for time steps %d...", id, self.extend_t)

    local layers = {}
    local inputs_p = {} --map:port of the TNN to layer ref and port
    local outputs_p = {}
    local dim_in = layer_conf.dim_in
    local dim_out = layer_conf.dim_out
    local parsed_conns = {}
    local _
    
    for id, _ in pairs(layer_conf.sub_layers.layers) do --caution: with this line, some layer not connected will be included
        discover(id, layers, layer_conf.sub_layers)
    end

    for _, ll in pairs(layer_conf.connections) do
        local id_from, port_from = parse_id(ll[1])
        local id_to, port_to = parse_id(ll[2])
        local time_to = ll[3] 

        print(id_from, id_to, time_to)

        local ref_from = discover(id_from, layers, layer_conf.sub_layers)
        local ref_to = discover(id_to, layers, layer_conf.sub_layers)
        
        if (id_from == "<input>") then
            if (dim_in[port_from] ~= ref_to.dim_in[port_to] or time_to ~= 0) then
                nerv.error("mismatch dimension or wrong time %s,%s,%d", ll[1], ll[2], ll[3])
            end
            inputs_p[port_from] = {["ref"] = ref_to, ["port"] = port_to}          
            ref_to.inputs_m[port_to] = {} --just a place holder
        elseif (id_to == "<output>") then
            if (dim_out[port_to] ~= ref_from.dim_out[port_from] or time_to ~= 0) then
                nerv.error("mismatch dimension or wrong time %s,%s,%d", ll[1], ll[2], ll[3])
            end
            outputs_p[port_to] = {["ref"] = ref_from, ["port"] = port_from}
            ref_from.outputs_m[port_from] = {} --just a place holder
        else
            local conn_now = { 
                ["src"] = {["ref"] = ref_from, ["port"] = port_from},
                ["dst"] = {["ref"] = ref_to, ["port"] = port_to},
                ["time"] = time_to
            }
            if (ref_to.dim_in[port_to] ~= ref_from.dim_out[port_from]) then
                nerv.error("mismatch dimension or wrong time %s,%s,%d", ll[1], ll[2], ll[3])
            end
            table.insert(parsed_conns, conn_now)
            ref_to.i_conns_p[conn_now.dst.port] = conn_now
            ref_from.o_conns_p[conn_now.src.port] = conn_now
        end
    end

    for id, ref in pairs(layers) do
        print(id, "#dim_in:", #ref.dim_in, "#dim_out:", #ref.dim_out, "#i_conns_p:", #ref.i_conns_p, "#o_conns_p", #ref.o_conns_p)
    end

    self.layers = layers
    self.inputs_p = inputs_p
    self.outputs_p = outputs_p
    self.id = id
    self.dim_in = dim_in
    self.dim_out = dim_out
    self.parsed_conns = parsed_conns
    self.gconf = global_conf
end

function TNN:init(batch_size, chunk_size)
    self.batch_size = batch_size
    self.chunk_size = chunk_size
    for i, conn in ipairs(self.parsed_conns) do --init storage for connections inside the NN
        local _, output_dim
        local ref_from, port_from, ref_to, port_to, time
        ref_from, port_from = conn.src.ref, conn.src.port
        ref_to, port_to = conn.dst.ref, conn.dst.port
        time = conn.time

        local dim = ref_from.dim_out[port_from]
        if (dim == 0) then
            nerv.error("layer %s has a zero dim port", ref_from.layer.id)
        end

        nerv.info("TNN initing storage %s->%s", ref_from.layer.id, ref_to.layer.id)
        ref_to.inputs_matbak_p[port_to] = self.gconf.cumat_type(batch_size, dim)
        self.make_initial_store(ref_from.outputs_m, port_from, dim, batch_size, chunk_size, self.extend_t, self.gconf, ref_to.inputs_m, port_to, time)
        ref_from.err_inputs_matbak_p[port_from] =  self.gconf.cumat_type(batch_size, dim)
        self.make_initial_store(ref_from.err_inputs_m, port_from, dim, batch_size, chunk_size, self.extend_t, self.gconf, ref_to.err_outputs_m, port_to, time)
    end

    self.outputs_m = {}
    self.err_inputs_m = {}
    for i = 1, #self.dim_out do --Init storage for output ports 
        local ref = self.outputs_p[i].ref
        local p = self.outputs_p[i].port
        self.make_initial_store(ref.outputs_m, p, self.dim_out[i], batch_size, chunk_size, self.extend_t, self.gconf, self.outputs_m, i, 0)
        self.make_initial_store(ref.err_inputs_m, p, self.dim_out[i], batch_size, chunk_size, self.extend_t, self.gconf, self.err_inputs_m, i, 0)
    end 

    self.inputs_m = {}
    self.err_outputs_m = {}
    for i = 1, #self.dim_in do --Init storage for input ports 
        local ref = self.inputs_p[i].ref
        local p = self.inputs_p[i].port
        self.make_initial_store(ref.inputs_m, p, self.dim_in[i], batch_size, chunk_size, self.extend_t, self.gconf, self.inputs_m, i, 0)
        self.make_initial_store(ref.err_outputs_m, p, self.dim_in[i], batch_size, chunk_size, self.extend_t, self.gconf, self.err_outputs_m, i, 0)
    end 

    for id, ref in pairs(self.layers) do --Calling init for child layers
        for i = 1, #ref.dim_in do
            if (ref.inputs_m[i] == nil or ref.err_outputs_m[i] == nil) then
                nerv.error("dangling input port %d of layer %s", i, id)
            end
        end
        for i = 1, #ref.dim_out do
            if (ref.outputs_m[i] == nil or ref.err_inputs_m[i] == nil) then
                nerv.error("dangling output port %d of layer %s", i, id)
            end
        end
        -- initialize sub layers
        nerv.info("TNN initing sub-layer %s", ref.id)       
        ref.layer:init(batch_size, chunk_size)
        collectgarbage("collect")
    end

    local flags_now = {}
    local flagsPack_now = {}
    for i = 1, chunk_size do
        flags_now[i] = {}
        flagsPack_now[i] = 0
    end

    self.feeds_now = {} --feeds is for the reader to fill
    self.feeds_now.inputs_m = self.inputs_m
    self.feeds_now.flags_now = flags_now
    self.feeds_now.flagsPack_now = flagsPack_now

    self:flush_all()
end

--[[
function DAGLayer:batch_resize(batch_size)
    self.gconf.batch_size = 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()

        if ref_from.outputs[port_from]:nrow() ~= batch_size and output_dim[port_from] > 0 then
            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
    end
    for id, ref in pairs(self.layers) do
        ref.layer:batch_resize(batch_size)
    end
    collectgarbage("collect")
end
]]--

function TNN:flush_all() --flush all history and activation
    local _, ref
    for _, ref in pairs(self.layers) do
        for i = 1, #ref.dim_in do
            for t = 1 - self.extend_t, self.chunk_size + self.extend_t do 
                ref.inputs_m[t][i]:fill(self.gconf.nn_act_default)
                if (ref.inputs_b[t] == nil) then
                    ref.inputs_b[t] = {}
                end
                ref.inputs_b[t][i] = false
                ref.err_outputs_m[t][i]:fill(0)
                if (ref.err_outputs_b[t] == nil) then
                    ref.err_outputs_b[t] = {}
                end
                ref.err_outputs_b[t][i] = false
            end
        end
        for i = 1, #ref.dim_out do
            for t = 1 - self.extend_t, self.chunk_size + self.extend_t do 
                ref.outputs_m[t][i]:fill(self.gconf.nn_act_default)
                if (ref.outputs_b[t] == nil) then
                    ref.outputs_b[t] = {}
                end
                ref.outputs_b[t][i] = false
                ref.err_inputs_m[t][i]:fill(0)
                if (ref.err_inputs_b[t] == nil) then
                    ref.err_inputs_b[t] = {}
                end
                ref.err_inputs_b[t][i] = false
            end
        end
    end
end

--reader: some reader
--Returns: bool, whether has new feed
--Returns: feeds, a table that will be filled with the reader's feeds
function TNN:getfeed_from_reader(reader)
    local feeds_now = self.feeds_now
    local got_new = reader:get_batch(feeds_now)
    return got_new, feeds_now
end

function TNN:move_right_to_nextmb(list_t) --move output history activations of 1..chunk_size to 1-chunk_size..0 
    if list_t == nil then
        list_t = {}
        for i = self.extend_t, 1, -1 do
            list_t[i] = 1 - i
        end
    end
    for i = 1, #list_t do
        t = list_t[i]
        if t < 1 - self.extend_t or t > 0 then
            nerv.error("MB move range error")
        end
        for id, ref in pairs(self.layers) do
            for p = 1, #ref.dim_out do
                ref.outputs_m[t][p]:copy_fromd(ref.outputs_m[t + self.chunk_size][p])
            end
        end
    end
end

function TNN:net_propagate() --propagate according to feeds_now
    for t = 1, self.chunk_size, 1 do
        for id, ref in pairs(self.layers) do
            for p = 1, #ref.dim_out do
                ref.outputs_b[t][p] = false
            end
            for p = 1, #ref.dim_in do
                ref.inputs_b[t][p] = false
            end
        end
    end

    local feeds_now = self.feeds_now
    for t = 1, self.chunk_size do --some layer maybe do not have inputs from time 1..chunk_size
        for id, ref in pairs(self.layers) do
            self:propagate_dfs(ref, t)
        end
    end
    for t = 1, self.chunk_size do
        if (bit.band(feeds_now.flagsPack_now[t], nerv.TNN.FC.HAS_INPUT) > 0) then
            for i = 1, #self.dim_in do
                local ref = self.inputs_p[i].ref
                local p = self.inputs_p[i].port
                ref.inputs_b[t][p] = true
                self:propagate_dfs(ref, t)
            end
        end
    end

    local flag_out = true 
    for t = 1, self.chunk_size do --check whether every output has been computed
        if (bit.band(feeds_now.flagsPack_now[t], nerv.TNN.FC.HAS_LABEL) > 0) then
            for i = 1, #self.dim_out do
                local ref = self.outputs_p[i].ref
                if (ref.outputs_b[t][1] ~= true) then
                    flag_out = false 
                    break
                end
            end
        end
    end

    if (flag_out == false) then
        nerv.error("some thing wrong, some labeled output is not propagated")
    end
end

--ref: the TNN_ref of a layer
--t: the current time to propagate
function TNN:propagate_dfs(ref, t)
    if (self:out_of_feedrange(t)) then
        return
    end
    if (ref.outputs_b[t][1] == true) then --already propagated, 1 is just a random port
        return
    end

    --print("debug dfs", ref.layer.id, t)

    local flag = true --whether have all inputs
    for _, conn in pairs(ref.i_conns_p) do
        local p = conn.dst.port
        if (not (ref.inputs_b[t][p] or self:out_of_feedrange(t - conn.time))) then
            flag = false
            break
        end
    end
    if (flag == false) then
        return
    end

    --ok, do propagate
    --print("debug ok, propagating");
    --The MB moving will cause bordering history to be changed, so it is more wise to flush the input activation
    if (bit.band(self.feeds_now.flagsPack_now[t], bit.bor(nerv.TNN.FC.SEQ_START, nerv.TNN.FC.SEQ_END)) > 0) then --flush cross-border history
        for i = 1, self.batch_size do
            local seq_start = bit.band(self.feeds_now.flags_now[t][i], nerv.TNN.FC.SEQ_START) 
            local seq_end = bit.band(self.feeds_now.flags_now[t][i], nerv.TNN.FC.SEQ_END) 
            if (seq_start > 0 or seq_end > 0) then
                for p, conn in pairs(ref.i_conns_p) do
                    if ((ref.i_conns_p[p].time > 0 and seq_start > 0) or (ref.i_conns_p[p].time < 0 and seq_end > 0)) then --cross-border, set to default
                        ref.inputs_m[t][p][i - 1]:fill(self.gconf.nn_act_default)
                    end
                end
            end
        end
    end
    self.gconf.timer:tic("tnn_actual_layer_propagate")
    ref.layer:propagate(ref.inputs_m[t], ref.outputs_m[t], t) --propagate!
    self.gconf.timer:toc("tnn_actual_layer_propagate")
    --[[ 
    if (bit.band(self.feeds_now.flagsPack_now[t], bit.bor(nerv.TNN.FC.SEQ_START, nerv.TNN.FC.SEQ_END)) > 0) then --restore cross-border history
        for i = 1, self.batch_size do
            local seq_start = bit.band(self.feeds_now.flags_now[t][i], nerv.TNN.FC.SEQ_START) 
            local seq_end = bit.band(self.feeds_now.flags_now[t][i], nerv.TNN.FC.SEQ_END) 
            if (seq_start > 0 or seq_end > 0) then
                for p, conn in pairs(ref.o_conns_p) do
                    if ((ref.o_conns_p[p].time > 0 and seq_end > 0) or (ref.o_conns_p[p].time < 0 and seq_start > 0)) then 
                        ref.outputs_m[t][p][i - 1]:fill(self.gconf.nn_act_default)                       
                    end
                end
            end
        end
    end
    ]]--
    --set input flag for future layers
    for i = 1, #ref.dim_out do
        if (ref.outputs_b[t][i] == true) then
            nerv.error("this time's outputs_b should be false")
        end
        ref.outputs_b[t][i] = true
    end
    
    --try dfs for further layers
    for _, conn in pairs(ref.o_conns_p) do
        --print("debug dfs-searching", conn.dst.ref.layer.id)
        conn.dst.ref.inputs_b[t + conn.time][conn.dst.port] = true
        self:propagate_dfs(conn.dst.ref, t + conn.time)
    end
end

--do_update: bool, whether we are doing back-propagate or updating the parameters
function TNN:net_backpropagate(do_update) --propagate according to feeds_now
    if do_update == nil then
        nerv.error("do_update should not be nil")
    end
    for t = 1, self.chunk_size, 1 do
        for id, ref in pairs(self.layers) do
            for p = 1, #ref.dim_out do
                ref.err_inputs_b[t][p] = false
            end
            for p = 1, #ref.dim_in do
                ref.err_outputs_b[t][p] = false
            end
        end
    end

    local feeds_now = self.feeds_now
    for t = 1, self.chunk_size do --some layer maybe do not have outputs from time 1..chunk_size
        for id, ref in pairs(self.layers) do
            self:backpropagate_dfs(ref, t, do_update)
        end
    end
    for t = 1, self.chunk_size do
        if bit.band(feeds_now.flagsPack_now[t], nerv.TNN.FC.HAS_LABEL) > 0 then
            for i = 1, #self.dim_out do
                local ref = self.outputs_p[i].ref
                local p = self.outputs_p[i].port
                ref.err_inputs_b[t][p] = true
                self:backpropagate_dfs(ref, t, do_update)
            end
        end
    end

    local flag_out = true 
    for t = 1, self.chunk_size do --check whether every output has been computed
        if bit.band(feeds_now.flagsPack_now[t], nerv.TNN.FC.HAS_INPUT) > 0 then
            for i = 1, #self.dim_in do
                local ref = self.inputs_p[i].ref
                if ref.err_outputs_b[t][1] ~= true then
                    flag_out = false 
                    break
                end
            end
        end
    end
    if (flag_out == false) then
        nerv.error("some thing wrong, some input is not back_propagated")
    end
end

--ref: the TNN_ref of a layer
--t: the current time to propagate
function TNN:backpropagate_dfs(ref, t, do_update)
    if do_update == nil then
        nerv.error("got a nil do_update")
    end
    if self:out_of_feedrange(t) then
        return
    end
    if ref.err_outputs_b[t][1] == true then --already back_propagated, 1 is just a random port
        return
    end

    --print("debug dfs", ref.layer.id, t)

    local flag = true --whether have all inputs
    for _, conn in pairs(ref.o_conns_p) do
        local p = conn.src.port
        if (not (ref.err_inputs_b[t][p] or self:out_of_feedrange(t + conn.time))) then
            flag = false
            break
        end
    end
    if (flag == false) then
        return
    end

    --ok, do back_propagate
    --print("debug ok, back-propagating(or updating)")
    if (do_update == false) then
        self.gconf.timer:tic("tnn_actual_layer_backpropagate")
        ref.layer:back_propagate(ref.err_inputs_m[t], ref.err_outputs_m[t], ref.inputs_m[t], ref.outputs_m[t], t)
        self.gconf.timer:toc("tnn_actual_layer_backpropagate")
        if self.clip_t > 0 then
            for _, conn in pairs(ref.i_conns_p) do
                local p = conn.dst.port --port for ref
                if conn.time ~= 0 then
                    --print("debug clip_t tnn", ref.id, "port:", p, "clip:", self.clip_t)
                    ref.err_outputs_m[t][p]:clip(-self.clip_t, self.clip_t)
                end
            end
        end
    else 
        --print(ref.err_inputs_m[t][1])
        self.gconf.timer:tic("tnn_actual_layer_update") 
        ref.layer:update(ref.err_inputs_m[t], ref.inputs_m[t], ref.outputs_m[t], t)
        self.gconf.timer:toc("tnn_actual_layer_update") 
    end

    if (do_update == false and bit.band(self.feeds_now.flagsPack_now[t], bit.bor(nerv.TNN.FC.SEQ_START, nerv.TNN.FC.SEQ_END)) > 0) then --flush cross-border errors
        for i = 1, self.batch_size do
            local seq_start = bit.band(self.feeds_now.flags_now[t][i], nerv.TNN.FC.SEQ_START) 
            local seq_end = bit.band(self.feeds_now.flags_now[t][i], nerv.TNN.FC.SEQ_END) 
            if (seq_start > 0 or seq_end > 0) then
                for p, conn in pairs(ref.i_conns_p) do
                    if ((ref.i_conns_p[p].time > 0 and seq_start > 0) or (ref.i_conns_p[p].time < 0 and seq_end > 0)) then --cross-border, set to zero
                        ref.err_outputs_m[t][p][i - 1]:fill(0)
                    end
                end
            end
        end
    end

    for i = 1, #ref.dim_in do
        if (ref.err_outputs_b[t][i] == true) then
            nerv.error("this time's outputs_b should be false")
        end
        ref.err_outputs_b[t][i] = true
    end
    
    --try dfs for further layers
    for _, conn in pairs(ref.i_conns_p) do
        --print("debug dfs-searching", conn.src.ref.layer.id)
        conn.src.ref.err_inputs_b[t - conn.time][conn.src.port] = true
        self:backpropagate_dfs(conn.src.ref, t - conn.time, do_update)
    end
end

--Return: nerv.ParamRepo
function TNN:get_params()
    local param_repos = {}
    for id, ref in pairs(self.layers) do
        table.insert(param_repos, ref.layer:get_params())
    end
    return nerv.ParamRepo.merge(param_repos)
end