DEXA Reporting Automation

1#Requires AutoHotkey v2.0
2#SingleInstance force
3
4; Version variable
5global VERSION := "6.06"
6
7global PatientAge := ""
8global PatientSex := ""
9global TScores := Map()
10global ZScores := Map()
11global OriginalReport := ""
12global FinalReport := ""
13global ImpressionInfo := ""  ; for diagnostic summary display
14global StatusCtrl := ""      ; GUI Status Control
15global DebugMode := false
16global SeenRegions := Map()  ; To track duplicates
17
18; GLOBAL SETTINGS FOR COLUMN MAPPING (Default: T is 1st score, Z is 2nd)
19global ColMap_T := 1
20global ColMap_Z := 2
21
22; Create GUI
23CreateGUI()
24
25CreateGUI() {
26    global StatusCtrl
27    ; Define helper text
28    helperText := "DEXA Parser v" . VERSION . " - Ready`n`n"
29        . "USAGE: Press Alt + d to process report`n"
30        . "(Hold Shift+Alt+d for Debug Mode)`n`n"
31        . "CRITERIA:`n"
32        . "• Female < 60: Z-score + T-score`n"
33        . "• Female ≥ 60: T-score only`n"
34        . "• Male < 50: Z-score only`n"
35        . "• Male ≥ 50: T-score only`n`n"
36        . "Works with Spine/Hip/Forearm DEXA scans`n"
37        . "Close window to exit."
38    
39    ; Create GUI window
40    myGui := Gui("+Resize +MinSize300x280", "DEXA Parser v" . VERSION)
41    myGui.MarginX := 10
42    myGui.MarginY := 10
43    
44    ; Set font
45    myGui.SetFont("s9", "Segoe UI")
46    
47    ; Add title
48    titleCtrl := myGui.Add("Text", "w320 h25 Center", "DEXA Parser Script")
49    titleCtrl.SetFont("s12 Bold")
50    
51    ; Add spacer
52    myGui.Add("Text", "h8")
53    
54    ; Add instructions text
55    myGui.Add("Text", "w320 h180", helperText)
56    
57    ; Add Status Bar
58    myGui.Add("Text", "w320 h1 0x10") ; Separator line
59    StatusCtrl := myGui.Add("Text", "w320 h20 vStatusText", "Status: Idle")
60    StatusCtrl.SetFont("s9 Italic")
61
62    ; Close handler
63    myGui.OnEvent("Close", (*) => ExitApp())
64    
65    ; Show GUI
66    myGui.Show("w340 h320")
67    
68    return myGui
69}
70
71UpdateStatus(text) {
72    global StatusCtrl
73    if IsObject(StatusCtrl)
74        StatusCtrl.Text := "Status: " . text
75}
76
77; Main Hotkey (Alt + d)
78!d:: {
79    RunParser(false)
80}
81
82; Debug Hotkey (Shift + Alt + d)
83+!d:: {
84    RunParser(true)
85}
86
87RunParser(debug) {
88    global DebugMode
89    DebugMode := debug
90    
91    UpdateStatus("Selecting text...")
92    
93    ; Clear Clipboard to prevent "Stale Data" race condition
94    A_Clipboard := ""
95    
96    ; Select All with increased delay for slow UIs
97    Send("^a")
98    Sleep(300) 
99    
100    Send("^c")
101    
102    ; Wait up to 2 seconds for NEW text to appear
103    if !ClipWait(2) {
104        UpdateStatus("Error: Clipboard timeout")
105        MsgBox("Failed to copy text. The clipboard did not update in time.", "Error", 0x10)
106        return
107    }
108
109    UpdateStatus("Parsing data...")
110    ParseDEXAReport()
111
112    ; Select all again and paste the final report to overwrite
113    if (FinalReport != "") {
114        UpdateStatus("Pasting report...")
115        Send("^a")
116        Sleep(300) ; Increased delay to ensure selection is registered
117        Send("^v")
118        Sleep(500)
119        UpdateStatus("Idle")
120    } else {
121        UpdateStatus("Aborted")
122    }
123}
124
125
126NormalizeWhitespace(text) {
127    ; Explicitly replace Non-Breaking Spaces (Chr 160) which RegEx \s might miss in some AHK versions
128    text := StrReplace(text, Chr(160), " ")
129    
130    text := RegExReplace(text, "\p{Zs}+", " ")
131    text := StrReplace(text, "`t", " ")
132    text := StrReplace(text, "`r", "")
133    text := RegExReplace(text, "[ -​]", " ")
134    text := RegExReplace(text, " +", " ")
135    return text
136}
137
138ParseDEXAReport() {
139    global PatientAge, PatientSex, TScores, ZScores, OriginalReport, FinalReport, ImpressionInfo, DebugMode, SeenRegions
140
141    if (A_Clipboard = "") {
142        MsgBox("Clipboard is empty or contains no text.", "DEXA Parser", 0x40)
143        return
144    }
145
146    OriginalReport := A_Clipboard
147    FinalReport := ""
148
149    ClipboardText := NormalizeWhitespace(A_Clipboard)
150    ClipboardText := RegExReplace(ClipboardText, ":[\s\t]+", ": ")
151    ClipboardText := NormalizeWhitespace(ClipboardText)
152    
153    if (DebugMode) {
154        MsgBox("Debug View - Normalized Text Start:`n`n" . SubStr(ClipboardText, 1, 500), "Debug", 0x40)
155    }
156
157    PatientAge := ""
158    PatientSex := ""
159    TScores.Clear()
160    ZScores.Clear()
161    SeenRegions.Clear()
162
163    if RegExMatch(ClipboardText, "Age:\s*(\d+)", &AgeMatch) {
164        PatientAge := AgeMatch[1]
165    }
166
167    if RegExMatch(ClipboardText, "Sex:\s*(\w+)", &SexMatch) {
168        PatientSex := SexMatch[1]
169    }
170
171    ParseBoneDensityTable(ClipboardText)
172
173    ; SANITY CHECK: Minimum Data Threshold
174    if (TScores.Count == 0) {
175        MsgBox("No bone density data found in selection.`n`nTroubleshooting:`n1. Ensure the 'Results' table is selected.`n2. Check if the table header contains 'Region'.`n3. Try Shift+Alt+D for Debug Mode.", "Parse Error", 0x10)
176        return
177    }
178    
179    ; Warn if very few regions found (possible bad copy)
180    if (TScores.Count < 2) {
181        result := MsgBox("Warning: Only " . TScores.Count . " valid body region found.`n(Usually expect Spine, Hips, etc.)`n`nProceed?", "Sanity Check", 0x34)
182        if (result == "No")
183            return
184    }
185
186    Impression := GenerateImpression()
187    
188    if (Impression = "")
189        return
190
191    FinalReport := InsertImpression(OriginalReport, Impression)
192
193    ; Copy to clipboard
194    A_Clipboard := FinalReport
195}
196
197ParseBoneDensityTable(Text) {
198    global TScores, ZScores, DebugMode, SeenRegions, ColMap_T, ColMap_Z
199    Lines := StrSplit(Text, "`n")
200    InResultsSection := false
201    HeaderFound := false
202
203    ; Reset column mapping to default (T first, Z second)
204    ColMap_T := 1
205    ColMap_Z := 2
206
207    for Line in Lines {
208        Line := Trim(Line, "`r `t")
209        if (Line = "")
210            continue
211
212        Line := RegExReplace(Line, "\s+", " ")
213
214        ; ROBUSTNESS 1: Flexible Header Detection
215        if (!InResultsSection && (RegExMatch(Line, "i)Region.*(BMD|T-?score|Z-?score)") 
216            || RegExMatch(Line, "i)Bone mineral density.*scores")
217            || RegExMatch(Line, "i)Bone Density Results:"))) {
218            
219            InResultsSection := true
220            HeaderFound := true
221            
222            ; Dynamic Mapping: Check position of "T-score" vs "Z-score" if present
223            PosT := InStr(Line, "T-score") ? InStr(Line, "T-score") : InStr(Line, "Tscore")
224            PosZ := InStr(Line, "Z-score") ? InStr(Line, "Z-score") : InStr(Line, "Zscore")
225
226            if (PosT > 0 && PosZ > 0 && PosZ < PosT) {
227                ColMap_T := 2
228                ColMap_Z := 1
229            }
230            continue
231        }
232
233        ; STOP parsing if we hit the footer, "Previous Exams", "Comparison", or FRAX
234        if (InResultsSection && (
235            InStr(Line, "World Health Organization")
236            || InStr(Line, "Comparison with Previous Exams")
237            || InStr(Line, "COMPARISON:")
238            || InStr(Line, "Change:")
239            || InStr(Line, "FRAX")
240        )) {
241            InResultsSection := false
242            return
243        }
244
245        if (InResultsSection && !InStr(Line, "Classification")) {
246            if (!ParseBoneDensityLine(Line)) {
247                InResultsSection := false
248                return 
249            }
250        }
251    }
252    
253    if (DebugMode && !HeaderFound) {
254        MsgBox("Debug Warning: Table Header NOT found.`nLooking for line containing 'Region' and 'BMD'/'Score'.", "Debug", 0x30)
255    }
256}
257
258ParseBoneDensityLine(Line) {
259    global TScores, ZScores, SeenRegions, ColMap_T, ColMap_Z
260    Line := Trim(Line)
261    Line := RegExReplace(Line, "\s+", " ")
262
263    ; Expanded Date Exclusion
264    ; Blocks: 02/02/2026, 2/2/26, 2026-02-02, 02-Feb-2026
265    if (RegExMatch(Line, "\d{1,2}/\d{1,2}/\d{2,4}") 
266        || RegExMatch(Line, "\d{4}-\d{2}-\d{2}") 
267        || RegExMatch(Line, "\d{2}-[A-Za-z]{3}-\d{4}"))
268        return true
269
270    ; --- ATTEMPT 1: Standard 3-Number Format (Region BMD T Z) ---
271    ; FIX V6: STRICT DECIMAL RULE
272    ; Requires `[0-9]*\.[0-9]+` (a number with a dot).
273    ; This ignores integers like "33", "2026", etc.
274    ; FIX V6.06: HYPHEN SUPPORT for Z-scores
275    if RegExMatch(Line, "^(.+?)\s+([0-9]*\.[0-9]+)[^\d\.-]+([0-9.-]+|[-])\s+([0-9.-]+|[-])", &Match) {
276        Region := Trim(Match[1])
277        Score1 := Match[3]
278        Score2 := Match[4]
279        
280        ; Handle hyphens as missing values
281        if (Score1 == "-") Score1 := ""
282        if (Score2 == "-") Score2 := ""
283        
284        TScore := (ColMap_T == 1) ? Score1 : Score2
285        ZScore := (ColMap_Z == 1) ? Score1 : Score2
286        
287        ProcessDataLine(Region, TScore, ZScore)
288        return true
289    }
290
291    ; --- ATTEMPT 2: "Greedy Score Search" (Catches lines like "L1, L2 -2.6, -2.7") ---
292    ; Matches a line starting with a word, followed by ANY sequence of decimal numbers
293    if RegExMatch(Line, "^([A-Za-z0-9 /,]+)\s+([+-]?\d+\.\d+)", &Match) {
294        Region := Trim(Match[1])
295        
296        ; Find ALL numbers in the line that look like scores
297        LowestFoundT := 1000
298        Pos := 1
299        FoundAny := false
300        
301        Loop {
302            ; Search for next float
303            Pos := RegExMatch(Line, "([+-]?\d+\.\d+)", &NumMatch, Pos)
304            if (!Pos)
305                break
306                
307            Val := NumMatch[1]
308            if (IsNumeric(Val) && Abs(Val) < 10) { ; Basic sanity check
309                if (Val < LowestFoundT)
310                    LowestFoundT := Val
311                FoundAny := true
312            }
313            Pos += StrLen(Val)
314        }
315
316        if (FoundAny) {
317            ; In this fallback format, we assume Z-scores are not reliable or present
318            ; So we only register the lowest found number as the T-Score.
319            ProcessDataLine(Region, LowestFoundT, "")
320            return true
321        }
322    }
323    
324    return true ; Continue parsing other lines
325}
326
327ProcessDataLine(Region, TScore, ZScore) {
328    global TScores, ZScores, SeenRegions
329
330    ; EXCLUSION LIST: Forearm artifacts and Ward's Triangle
331    if (InStr(Region, "Total Forearm") 
332        || InStr(Region, "UD Forearm") 
333        || InStr(Region, "Ultra") 
334        || InStr(Region, "Ward"))
335        return
336
337    ; Physiological Check
338    if (TScore != "" && Abs(TScore) > 10)
339        return
340    if (ZScore != "" && Abs(ZScore) > 10)
341        return
342
343    ; Duplicate Region Check
344    if (SeenRegions.Has(Region)) {
345        return false ; STOP parsing
346    }
347
348    if (TScore != "")
349        TScores[Region] := TScore
350    if (ZScore != "")
351        ZScores[Region] := ZScore
352        
353    SeenRegions[Region] := true
354}
355
356IsNumeric(str) {
357    try {
358        if (str == "" || str == "-") return false
359        Float(str)
360        return true
361    } catch {
362        return false
363    }
364}
365
366GenerateImpression() {
367    global TScores, ZScores, PatientAge, PatientSex, ImpressionInfo
368
369    if !IsObject(TScores)
370        TScores := Map()
371    if !IsObject(ZScores)
372        ZScores := Map()
373    
374    ; Safety check for Age
375    if (!PatientAge || PatientAge = 0 || PatientAge = "") {
376        ib := InputBox("Patient Age could not be detected automatically.`nPlease enter Age:", "DEXA Parser", "w250 h130 +AlwaysOnTop")
377        if (ib.Result = "Cancel" || ib.Value = "") {
378            MsgBox("Processing Cancelled: No Age Provided.")
379            return "" 
380        }
381        PatientAge := ib.Value
382    }
383    
384    ; SANITY CHECK: Age Plausibility
385    if (PatientAge < 18 || PatientAge > 110) {
386        ib := InputBox("Warning: Patient Age is " . PatientAge . ".`nIs this correct?`n`nEdit below if needed, or Cancel to abort.", "Age Check", "w250 h140 +AlwaysOnTop", PatientAge)
387        if (ib.Result = "Cancel")
388            return ""
389        PatientAge := ib.Value
390    }
391    
392    if !IsSet(PatientSex) || PatientSex = ""
393        PatientSex := ""
394
395    lowestT := 1000
396    lowestTRegion := ""
397    
398    lowestZ := 1000
399    lowestZRegion := ""
400
401    for region, val in TScores {
402        score := Round(val, 1)
403        if (score < lowestT) {
404            lowestT := score
405            lowestTRegion := region
406        }
407    }
408    
409    ; Handle missing Z-scores safely
410    hasZ := (ZScores.Count > 0)
411    if (hasZ) {
412        for region, val in ZScores {
413            score := Round(val, 1)
414            if (score < lowestZ) {
415                lowestZ := score
416                lowestZRegion := region
417            }
418        }
419    }
420
421    age := PatientAge + 0
422    sex := Trim(PatientSex)
423    
424    impression := "TECHNICAL LIMITATIONS: None`n"
425        . "------------------------------------------------------------------------------`n"
426        . "IMPRESSION:`n`n"
427
428    ; ALERT: Missing Z-Scores for Young Patients
429    if (age < 50 && !hasZ) {
430        MsgBox("ALERT: Patient is " . age . " years old but NO Z-scores were found in the report.`n`nThe impression will use T-scores, but clinical correlation is advised.", "Missing Data", 0x30 + 0x40000)
431    }
432
433    ; Women under 60
434    if (sex ~= "i)^F" && age < 60) {
435        if (hasZ) {
436            zDiag := (lowestZ <= -2.0) ? "Below the expected range for age in premenopausal women" : "Within the expected range for age in premenopausal women"
437            zDiag .= " (lowest Z-score " . lowestZ . " at " . lowestZRegion . ")."
438            impression .= zDiag . "`n"
439        }
440
441        if (lowestT <= -2.5) {
442            tDiag := "Osteoporosis in postmenopausal women"
443            siteText := " (" . lowestTRegion . ")"
444        } else if (lowestT < -1.0) {
445            tDiag := "Osteopenia in postmenopausal women"
446            siteText := " (" . lowestTRegion . ")"
447        } else {
448            tDiag := "Normal bone density in postmenopausal women"
449            siteText := ""
450        }
451        
452        impression .= tDiag . " based on the lowest T-score" . siteText . " using the World Health Organization criteria.`n`n"
453
454        impression .= "In premenopausal women, Z-scores are preferred and the WHO classification is not applicable. "
455            . "In these patients, a Z-score of -2.0 or lower is defined as “below the expected range for age” and above -2.0 is “within the expected range for age.” "
456            . "The diagnosis of osteoporosis cannot be made on the basis of bone mineral density alone.`n"
457    }
458
459    ; Men under 50
460    else if (sex ~= "i)^M" && age < 50) {
461        if (hasZ) {
462            zDiag := (lowestZ <= -2.0) ? "Below the expected range for age" : "Within the expected range for age"
463            zDiag .= " (lowest Z-score " . lowestZ . " at " . lowestZRegion . ")."
464            impression .= zDiag . "`n`n"
465        } else {
466             impression .= "Z-SCORES NOT AVAILABLE for this patient. T-scores reported below.`n`n"
467             ; Fallback to T-score logic for clarity
468             if (lowestT <= -2.5) {
469                classification := "Osteoporosis"
470                siteText := " (" . lowestTRegion . ")"
471             } else if (lowestT < -1.0) {
472                classification := "Osteopenia"
473                siteText := " (" . lowestTRegion . ")"
474             } else {
475                classification := "Normal bone density"
476                siteText := ""
477             }
478             impression .= classification . " based on the lowest T-score" . siteText . ".`n`n"
479        }
480
481        impression .= "In male patients below age 50, Z-scores are preferred and the WHO classification is not applicable. "
482            . "In these patients, a Z-score of -2.0 or lower is defined as “below the expected range for age” and above -2.0 is “within the expected range for age.” "
483            . "The diagnosis of osteoporosis cannot be made on the basis of bone mineral density alone.`n"
484    }
485
486    ; Women 60+ or Men 50+
487    else {
488        if (lowestT <= -2.5) {
489            classification := "Osteoporosis"
490            siteText := " (" . lowestTRegion . ")"
491        } else if (lowestT < -1.0) {
492            classification := "Osteopenia"
493            siteText := " (" . lowestTRegion . ")"
494        } else {
495            classification := "Normal bone density"
496            siteText := ""
497        }
498
499        impression .= classification . " based on the lowest T-score" . siteText . " using the World Health Organization criteria.`n"
500    }
501
502    impression .= "------------------------------------------------------------------------------"
503    return impression
504}
505
506InsertImpression(text, impression) {
507    searchPatterns := [
508        "Osteoporosis (T-score at or below -2.5).",
509        "FRAX(R) Estimated 10-year Fracture Risk:",
510        "Comparison With Previous Exams:",
511        "Electronically Signed",
512        "Signed by"
513    ]
514    
515    insertIndex := 0
516    matchLen := 0
517    foundPattern := ""
518
519    for pattern in searchPatterns {
520        if (pos := InStr(text, pattern)) {
521            insertIndex := pos
522            matchLen := StrLen(pattern)
523            foundPattern := pattern
524            break
525        }
526    }
527
528    if (insertIndex > 0) {
529        if (foundPattern = "Osteoporosis (T-score at or below -2.5).") {
530             newlinePos := InStr(text, "`n", , insertIndex + matchLen)
531             splitPos := (newlinePos > 0) ? newlinePos + 1 : insertIndex + matchLen + 1
532             return SubStr(text, 1, splitPos - 1) . "`n`n" . impression . "`n`n" . SubStr(text, splitPos)
533        } else {
534            return SubStr(text, 1, insertIndex - 1) . "`n" . impression . "`n`n" . SubStr(text, insertIndex)
535        }
536    } else {
537        MsgBox("Could not find standard insertion point. Appending to bottom.", "DEXA Parser", 0x30 + 0x40000)
538        return text . "`n`n" . impression
539    }
540}