geddes 0.1.5

A Rust library for parsing XRD pattern files
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336

use crate::error::GeddesError;
use quick_xml::events::Event;
use quick_xml::Reader;
use std::io::{BufRead, BufReader, Read, Seek};
use zip::ZipArchive;

/// Intermediate structure to hold parsed data before converting to the public Pattern struct.
#[derive(Debug)]
pub struct ParsedData {
    pub x: Vec<f64>,
    pub y: Vec<f64>,
    pub e: Option<Vec<f64>>,
}

/// Helper to parse x, y, and optional e from string parts.
fn parse_columns(parts: &[&str], x: &mut Vec<f64>, y: &mut Vec<f64>, e: &mut Vec<f64>) {
    if parts.len() >= 2 {
        if let (Ok(val_x), Ok(val_y)) = (parts[0].parse::<f64>(), parts[1].parse::<f64>()) {
            x.push(val_x);
            y.push(val_y);
            if parts.len() >= 3 {
                if let Ok(val_e) = parts[2].parse::<f64>() {
                    e.push(val_e);
                }
            }
        }
    }
}

/// Parses standard XY files (two or three columns: x, y, [e]).
///
/// Ignores lines starting with '#' or '!'.
pub fn parse_xy<R: Read>(reader: R) -> Result<ParsedData, GeddesError> {
    let reader = BufReader::new(reader);
    let mut x = Vec::new();
    let mut y = Vec::new();
    let mut e = Vec::new();

    for line in reader.lines() {
        let line = line?;
        let line = line.trim();
        if line.is_empty() || line.starts_with('#') || line.starts_with('!') {
            continue;
        }
        let parts: Vec<&str> = line.split_whitespace().collect();
        parse_columns(&parts, &mut x, &mut y, &mut e);
    }

    let has_error = !e.is_empty() && e.len() == x.len();
    Ok(ParsedData {
        x,
        y,
        e: if has_error { Some(e) } else { None },
    })
}

/// Parses CSV files.
///
/// Supports comma or whitespace as delimiters.
pub fn parse_csv<R: Read>(reader: R) -> Result<ParsedData, GeddesError> {
    let reader = BufReader::new(reader);
    let mut x = Vec::new();
    let mut y = Vec::new();
    let mut e = Vec::new();

    for line in reader.lines() {
        let line = line?;
        let line = line.trim();
        if line.is_empty() || line.starts_with('#') || line.starts_with('!') {
            continue;
        }
        // Support both comma-separated and whitespace-separated CSV-like files.
        let parts: Vec<&str> = line
            .split(|c: char| c == ',' || c.is_whitespace())
            .map(|p| p.trim())
            .filter(|p| !p.is_empty())
            .collect();
        parse_columns(&parts, &mut x, &mut y, &mut e);
    }

    let has_error = !e.is_empty() && e.len() == x.len();
    Ok(ParsedData {
        x,
        y,
        e: if has_error { Some(e) } else { None },
    })
}

/// Parses Rigaku RASX files (zipped XML/text format).
///
/// Looks for a `Profile*.txt` file inside the archive.
pub fn parse_rasx<R: Read + Seek>(reader: R) -> Result<ParsedData, GeddesError> {
    let mut archive = ZipArchive::new(reader)?;

    let names: Vec<String> = (0..archive.len())
        .filter_map(|i| archive.by_index(i).ok().map(|f| f.name().to_string()))
        .collect();

    // Prioritize Data0/Profile0.txt, or find any Profile*.txt
    let profile_name = names
        .iter()
        .find(|n| n.as_str() == "Data0/Profile0.txt")
        .or_else(|| {
            names
                .iter()
                .find(|n| n.contains("Profile") && n.ends_with(".txt"))
        })
        .ok_or_else(|| GeddesError::FileNotFoundInArchive("Profile*.txt".to_string()))?;

    let file = archive.by_name(profile_name)?;
    let reader = BufReader::new(file);

    let mut x = Vec::new();
    let mut y = Vec::new();

    for line in reader.lines() {
        let line = line?;
        let line = line.trim();
        if line.is_empty() {
            continue;
        }
        let parts: Vec<&str> = line.split_whitespace().collect();
        if parts.len() >= 2 {
            if let (Ok(val_x), Ok(val_y)) = (parts[0].parse::<f64>(), parts[1].parse::<f64>()) {
                x.push(val_x);
                y.push(val_y);
            }
        }
    }
    Ok(ParsedData { x, y, e: None })
}

/// Parses Panalytical XRDML files (XML-based).
///
/// Extracts the 2Theta start/end positions and the intensities list.
pub fn parse_xrdml<R: Read>(reader: R) -> Result<ParsedData, GeddesError> {
    let reader = BufReader::new(reader);
    let mut xml = Reader::from_reader(reader);
    xml.config_mut().trim_text(true);

    let mut buf = Vec::new();
    let mut intensities = Vec::new();
    let mut in_intensities = false;
    let mut in_positions_2theta = false;
    let mut capture_start = false;
    let mut capture_end = false;
    let mut start_pos: Option<f64> = None;
    let mut end_pos: Option<f64> = None;

    loop {
        match xml.read_event_into(&mut buf) {
            Ok(Event::Start(e)) => match e.local_name().as_ref() {
                b"positions" => {
                    in_positions_2theta = false;
                    for attr in e.attributes() {
                        let attr = attr.map_err(|err| {
                            GeddesError::Parse(format!("XRDML attribute error: {err}"))
                        })?;
                        if attr.key.as_ref() == b"axis" {
                            let axis = attr
                                .unescape_value()
                                .map_err(|err| {
                                    GeddesError::Parse(format!(
                                        "XRDML attribute decode error: {err}"
                                    ))
                                })?
                                .into_owned();
                            if axis == "2Theta" {
                                in_positions_2theta = true;
                            }
                        }
                    }
                }
                b"startPosition" => {
                    if in_positions_2theta {
                        capture_start = true;
                    }
                }
                b"endPosition" => {
                    if in_positions_2theta {
                        capture_end = true;
                    }
                }
                b"intensities" => {
                    in_intensities = true;
                }
                _ => {}
            },
            Ok(Event::Text(e)) => {
                let text = e
                    .decode()
                    .map_err(|err| GeddesError::Parse(format!("XRDML text decode error: {err}")))?;
                let text = text.trim();
                if text.is_empty() {
                    // Skip empty text nodes.
                } else if capture_start {
                    start_pos = Some(text.parse::<f64>().map_err(|_| {
                        GeddesError::Parse("XRDML invalid 2Theta start position".into())
                    })?);
                } else if capture_end {
                    end_pos = Some(text.parse::<f64>().map_err(|_| {
                        GeddesError::Parse("XRDML invalid 2Theta end position".into())
                    })?);
                } else if in_intensities {
                    for part in text.split_whitespace() {
                        if let Ok(value) = part.parse::<f64>() {
                            intensities.push(value);
                        }
                    }
                }
            }
            Ok(Event::End(e)) => match e.local_name().as_ref() {
                b"positions" => {
                    in_positions_2theta = false;
                }
                b"startPosition" => {
                    capture_start = false;
                }
                b"endPosition" => {
                    capture_end = false;
                }
                b"intensities" => {
                    in_intensities = false;
                    if !intensities.is_empty() && start_pos.is_some() && end_pos.is_some() {
                        break;
                    }
                }
                _ => {}
            },
            Ok(Event::Eof) => break,
            Err(err) => {
                return Err(GeddesError::Parse(format!("XRDML parse error: {err}")));
            }
            _ => {}
        }
        buf.clear();
    }

    let start = start_pos
        .ok_or_else(|| GeddesError::Parse("XRDML missing 2Theta start position".into()))?;
    let end =
        end_pos.ok_or_else(|| GeddesError::Parse("XRDML missing 2Theta end position".into()))?;

    if intensities.is_empty() {
        return Err(GeddesError::Parse("XRDML intensities not found".into()));
    }

    let mut x = Vec::with_capacity(intensities.len());
    if intensities.len() == 1 {
        x.push(start);
    } else {
        let step = (end - start) / (intensities.len() as f64 - 1.0);
        for i in 0..intensities.len() {
            x.push(start + (i as f64) * step);
        }
    }

    Ok(ParsedData {
        x,
        y: intensities,
        e: None,
    })
}

/// Parses GSAS RAW files.
///
/// Expects a `BANK` header line to determine start angle and step size.
pub fn parse_gsas_raw<R: Read>(reader: R) -> Result<ParsedData, GeddesError> {
    let reader = BufReader::new(reader);
    let mut lines = reader.lines();

    let mut start = 0.0;
    let mut step = 0.0;

    let mut header_found = false;

    for line_res in lines.by_ref() {
        let line = line_res?;
        if line.starts_with("BANK") {
            let parts: Vec<&str> = line.split_whitespace().collect();
            // BANK 1 4941 494 CONST 1600.0 1.7 0.0 0.0 STD
            if parts.len() >= 7 {
                let start_raw = parts[5]
                    .parse::<f64>()
                    .map_err(|_| GeddesError::Parse("Invalid start".into()))?;
                let step_raw = parts[6]
                    .parse::<f64>()
                    .map_err(|_| GeddesError::Parse("Invalid step".into()))?;

                // GSAS standard: centidegrees
                start = start_raw / 100.0;
                step = step_raw / 100.0;
                header_found = true;
                break;
            }
        }
    }

    if !header_found {
        return Err(GeddesError::Parse(
            "BANK header not found in RAW file".into(),
        ));
    }

    let mut y = Vec::new();

    for line in lines {
        let line = line?;
        if line.starts_with("BANK") {
            break;
        }
        let parts = line.split_whitespace();
        for part in parts {
            if let Ok(val) = part.parse::<f64>() {
                y.push(val);
            }
        }
    }

    // Generate x
    let mut x = Vec::with_capacity(y.len());
    for i in 0..y.len() {
        x.push(start + (i as f64) * step);
    }

    Ok(ParsedData { x, y, e: None })
}

/// Parses Bruker binary RAW files.
///
/// (Currently a placeholder returning an error)
pub fn parse_bruker_raw<R: Read>(_reader: R) -> Result<ParsedData, GeddesError> {
    Err(GeddesError::Parse(
        "Bruker binary RAW format not yet supported".into(),
    ))
}