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graph thinning
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Update main.rs

Update main.rs

wip

wip

Thinning bug

wip2 try_to_read_protocol_name

wip try_to_read_protocol_name
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@Evgenii-Barannik
Evgenii-Barannik committed Oct 29, 2023
1 parent 58d1144 commit 395823a
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Showing 2 changed files with 93 additions and 35 deletions.
5 changes: 5 additions & 0 deletions src/dim_analysis.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -448,3 +448,8 @@ pub fn try_to_read_reference_time(read_map: &Map<String, Value>) -> Option<Primi
}
}

pub fn try_to_read_protocol_name<'a>(map: &'a toml::value::Table) -> Option<&str> {
map.get("protocol").and_then(|value| value.as_table())
.and_then(|p| p.get("name"))
.and_then(|n| n.as_str())
}
123 changes: 88 additions & 35 deletions src/main.rs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,7 @@ const OUTPUT_GENEALOGY_DIR: &str = "output/genealogy/";
const OUTPUT_QRCODES_DIR: &str = "output/qrcodes/";

const GENEALOGY_NAME: &str = "genealogy";
const GENEALOGY_NAME_THINNED: &str = "genealogy-thinned";
const YEAST_PAGE_PATH: &str = "../content/info/yeasts.md";
const DOT_REPLACEMENT: &str =r##"
digraph {
Expand Down Expand Up @@ -145,18 +146,66 @@ fn tomls_into_nodes_and_links (input_dir: &str) -> (Nodes, HashMap<String, Strin
local_links_to_nodes.insert(id.unwrap(), String::from(file.canonicalize().unwrap().to_str().unwrap()));
} else { log_warnings( &format!("{:<25} {:<25} {:?}", "Parent or participants", "missing from", file));}
},
(_, _, None, _, _) => {log_warnings( &format!("{:<25} {:<25} {:?}", "Time and parent or participants)", "missing from", file) )}
(_, _, None, _, _) => {log_warnings( &format!("{:<25} {:<25} {:?}", "Time and parent or participants", "missing from", file) )}
}
}
}
println!("TOML files converted into checked nodes: {:?}", checked_nodes.len());
println!("Checked nodes created: {:?}", checked_nodes.len());
(checked_nodes, local_links_to_nodes)
}

fn node_should_remain_after_thinning (toml_map: &Map<String, Value>) -> bool {
let maybe_protocol_name = try_to_read_protocol_name(&toml_map);
let maybe_medium = try_to_read_field_as_string(&toml_map, "medium");

if maybe_protocol_name.unwrap_or("None") == "package" ||
maybe_medium.unwrap_or(String::from("None")) == "slant" {
true
} else {
false
}
}

fn thin_out_components(components: HashMap<String, Nodes> ) -> HashMap<String, Nodes> {
let mut thinned_components: HashMap<String, Nodes> = HashMap::new();
for (ancestor_node_id, nodes) in components {
let mut thinned_nodes: Nodes = HashMap::new();

let graph = build_digraphmap(nodes.clone());
let reversed_graph = Reversed(&graph); // We be used to go back to find new parent
let mut dfs = Dfs::new(&graph, &ancestor_node_id);

while let Some(id) = dfs.next(&graph) { // First iteration is trivial, gives the starting node itself. (id == ancestor_node_id)
let toml_map = nodes.get(id).unwrap();

if node_should_remain_after_thinning(toml_map) {
if try_to_read_field_as_string(&toml_map, "parent").unwrap() == "new" {
thinned_nodes.insert(id.to_string().clone(), toml_map.clone());
} else {
// Here we found node that should remain, but with `parent != "new"`
// We will walk back to find what new parent it should have on thinned graph.
let mut reverse_dfs = Dfs::new(&reversed_graph, &id);
reverse_dfs.next(&reversed_graph); // We skip first (trivial) iteration — it is the starting node itself.
while let Some(id_reverse) = reverse_dfs.next(&reversed_graph) { // Search back for the new parent
let toml_map_reverse = nodes.get(id_reverse).unwrap();
if node_should_remain_after_thinning(toml_map_reverse) {
let mut toml_map_mod = toml_map.clone();
toml_map_mod.insert(String::from("parent"), Value::String(String::from(id_reverse))); // Modify node
thinned_nodes.insert(id.to_string().clone(), toml_map_mod);
break
}
}
}
}
}
thinned_components.insert(ancestor_node_id, thinned_nodes);
}
thinned_components
}

fn nodes_into_components(nodes: Nodes, dust_mode: bool) -> HashMap<String, Nodes> {
// Splits nodes into connectivity components (dust_mode == false) or just dust (dust_mode == true).
// With (dust_mode == true) each component recieves exactly one Node.
// Thus (dust_mode == true) allows to fit each Node independently when we later fit components.
let mut components: HashMap<String, Nodes> = HashMap::new();
let graph = build_digraphmap(nodes.clone());
let reversed_graph = Reversed(&graph);
Expand All @@ -174,7 +223,6 @@ fn nodes_into_components(nodes: Nodes, dust_mode: bool) -> HashMap<String, Nodes
.or_insert_with(HashMap::new)
.insert(id, toml_map);
}
println!("(Connectivity) components created from checked nodes: {}", components.len());
log_component_separation_results(&components);
components
}
Expand Down Expand Up @@ -224,7 +272,6 @@ fn components_into_problems(components: HashMap<String, Nodes>) -> HashMap<Strin
});
}
}
println!("(Connectivity) components converted into optimization problems: {:?}", problems_for_components.len());
problems_for_components
}

Expand Down Expand Up @@ -597,14 +644,9 @@ fn plot_genealogy(pathname: String, nodes: Nodes, file_links: HashMap<String, St
let medium = toml_map.get("medium").unwrap().as_str().unwrap();
if let Some(colour) = colours_for_media.get(medium) {
let link = format!("file://{}", file_links.get(captured_id).unwrap());

let maybe_protocol = try_to_read_field_as_map(&toml_map, "protocol");
let shape_name = maybe_protocol
.and_then(|map| map.get("name"))
.and_then(|v| v.as_str())
.unwrap_or("ellipse");

let shape = shapes_for_protocols.get(shape_name).unwrap_or(&"ellipse");

let maybe_protocol_name = try_to_read_protocol_name(&toml_map);
let shape = shapes_for_protocols.get(maybe_protocol_name.unwrap_or("ellipse")).unwrap_or(&"ellipse");
let pattern_with_colour = format!(r#"{} [label="{}", URL="{}", fillcolor={}, shape={}]"#, captured_nodenumber, captured_id, link, colour, shape);
content = content.replace(&node_captures[0], &pattern_with_colour);
}
Expand All @@ -621,11 +663,7 @@ fn plot_genealogy(pathname: String, nodes: Nodes, file_links: HashMap<String, St

fn find_correct_organoleptic_node_in_component(component_nodes: &Nodes) -> Option<Map<String, Value>> {
for (_, toml_map) in component_nodes.iter() {
let maybe_protocol_name = try_to_read_field_as_map(toml_map, "protocol")
.and_then(|p| p.get("name"))
.and_then(|n| n.as_str());

match maybe_protocol_name {
match try_to_read_protocol_name(toml_map) {
Some(protocol_name) if protocol_name != "slant-qa" => {
if let Some(medium) = try_to_read_field_as_string(&toml_map, "medium") {
if medium == "organoleptic" {return Some(toml_map.clone()); }
Expand Down Expand Up @@ -657,18 +695,16 @@ fn populate_site_pages(nodes: Nodes, components: &HashMap<String, Nodes>, soluti
//// Filter for items for yeast page with depth 1:
let mut depth1_items = HashMap::new();
for (id, toml_map) in ordered_nodes.clone().into_iter(){
let maybe_protocol = try_to_read_field_as_map(&toml_map, "protocol");
if let Some(protocol) = maybe_protocol {
if protocol.get("name").unwrap().as_str().unwrap() == "package" {
let ancestors_id = components.iter()
.find(|&(_, nodes_map)| nodes_map.contains_key(id))
.map(|(component_id, nodes_map)| {component_id.clone()})
.unwrap();

let ancestors_toml_map = nodes.get(ancestors_id.as_str()).unwrap();
let character = try_to_read_field_as_string(ancestors_toml_map, "character").unwrap();
depth1_items.insert(ancestors_id, character);
}
let maybe_protocol_name = try_to_read_protocol_name(&toml_map);
if let Some("package") = maybe_protocol_name {
let ancestors_id = components.iter()
.find(|&(_, nodes_map)| nodes_map.contains_key(id))
.map(|(component_id, nodes_map)| {component_id.clone()})
.unwrap();

let ancestors_toml_map = nodes.get(ancestors_id.as_str()).unwrap();
let character = try_to_read_field_as_string(ancestors_toml_map, "character").unwrap();
depth1_items.insert(ancestors_id, character);
}
}
let ordered_depth1_items: BTreeMap<_, _> = depth1_items.into_iter()
Expand Down Expand Up @@ -768,11 +804,24 @@ fn populate_site_pages(nodes: Nodes, components: &HashMap<String, Nodes>, soluti
}
}

fn flatten_components(components: HashMap<String, Nodes>) -> Nodes {
let mut flat_nodes = HashMap::new();

for (_ancestor_id, component) in components {
for (id, toml_map) in component {
flat_nodes.insert(id, toml_map);
}
}
flat_nodes
}

fn main() {
let (nodes, local_file_links) = tomls_into_nodes_and_links(INPUT_DIR);
let components = nodes_into_components(nodes.clone(), false);
println!("Connectivity components created from checked nodes: {}", components.len());
let problems = components_into_problems(components.clone());

println!("Connectivity components converted into optimization problems: {:?}", problems.len());

let mut total_cost: f64 = 0.0;
let mut solutions: HashMap<String, NelderMeadComponentSolution> = HashMap::new();
for (component_id, component_problem) in problems {
Expand All @@ -783,13 +832,17 @@ fn main() {
}
println!("Total cost for all optimization problems: {:.4}", total_cost);

for (component_id, component) in &components {
let main_genealogy_pathname = OUTPUT_DIR.to_owned() + GENEALOGY_NAME;
plot_genealogy(main_genealogy_pathname, nodes.clone(), local_file_links.clone());

let thinned_components = thin_out_components(components.clone());
println!("Nodes left after thinning: {:?}", flatten_components(thinned_components.clone()).len());
for (component_id, component) in &thinned_components {
let genealogy_pathname = OUTPUT_GENEALOGY_DIR.to_owned() + "genealogy-" + &component_id;
plot_genealogy(genealogy_pathname, component.clone(), local_file_links.clone());
}
let main_genealogy_pathname = OUTPUT_DIR.to_owned() + GENEALOGY_NAME;
plot_genealogy(main_genealogy_pathname, nodes.clone(), local_file_links.clone());
println!("Genealogy graph plotted using graphwiz.");
let thinned_genealogy_pathname = OUTPUT_DIR.to_owned() + GENEALOGY_NAME_THINNED;
plot_genealogy(thinned_genealogy_pathname, flatten_components(thinned_components.clone()), local_file_links.clone());

if Path::new(&YEAST_PAGE_PATH).exists() {
println!("Yeast page is found at '{}'. Populating it with data.", YEAST_PAGE_PATH);
Expand Down

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