From 27a6d505eb853cb3a22a142ccef2b7198ad8c58b Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Sat, 5 Jan 2019 11:26:16 -0500
Subject: [PATCH 01/23] Add ccd_temp_acq to values calculated in calc_ccd_temps

---
 starcheck/calc_ccd_temps.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/starcheck/calc_ccd_temps.py b/starcheck/calc_ccd_temps.py
index 6fb24f9b..c10cbbb5 100755
--- a/starcheck/calc_ccd_temps.py
+++ b/starcheck/calc_ccd_temps.py
@@ -210,6 +210,7 @@ def get_interval_data(intervals, times, ccd_temp, obsreqs=None):
             obstemps[str(interval['obsid'])] = obs
             continue
         obs['ccd_temp'] = np.max(ok_temps)
+        obs['ccd_temp_acq'] = np.max(ok_temps[0:2]) if len(ok_temps) > 1 else obs['ccd_temp']
         obs['n100_warm_frac'] = dark_model.get_warm_fracs(
             100, interval['tstart'], np.max(ok_temps))
         # If we have an OR list, the obsid is in that list, and the OR list has zero-offset keys

From 46c8943ebfa5f97bd89f27fd1d587bb3b91e7350 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Sat, 5 Jan 2019 11:29:16 -0500
Subject: [PATCH 02/23] Use proseco for P_ACQ calculations

---
 .../src/lib/Ska/Starcheck/FigureOfMerit.pm    | 101 ----------
 starcheck/src/lib/Ska/Starcheck/Obsid.pm      | 189 +++++++++++++++++-
 starcheck/src/starcheck.pl                    |   5 +-
 3 files changed, 185 insertions(+), 110 deletions(-)
 delete mode 100644 starcheck/src/lib/Ska/Starcheck/FigureOfMerit.pm

diff --git a/starcheck/src/lib/Ska/Starcheck/FigureOfMerit.pm b/starcheck/src/lib/Ska/Starcheck/FigureOfMerit.pm
deleted file mode 100644
index c4d99591..00000000
--- a/starcheck/src/lib/Ska/Starcheck/FigureOfMerit.pm
+++ /dev/null
@@ -1,101 +0,0 @@
-package Ska::Starcheck::FigureOfMerit;
-##*****************************************************************************************
-#figure_of_merit.pm - Generates a probabilistic figure of merit for star catalogs 
-#                     within starcheck. 
-#
-#                     Outputs an array of:
-#                            the log probability of bright star hold
-#                            the expected number of acquisition stars identified
-#
-#                     Individual star probabilities are hard coded and will need
-#                     regular updates.
-#
-##*****************************************************************************************
-
-use strict;
-use List::Util qw(min sum);
-
-use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
-
-require Exporter;
-
-our @ISA = qw(Exporter);
-our @EXPORT = qw();
-our @EXPORT_OK = qw( make_figure_of_merit set_dynamic_mag_limits );
-our %EXPORT_TAGS = ( all => \@EXPORT_OK );
-
-use Inline Python => q{
-
-from chandra_aca.star_probs import acq_success_prob, prob_n_acq, mag_for_p_acq
-
-def _mag_for_p_acq(p_acq, date, t_ccd):
-    return mag_for_p_acq(p_acq, date.decode(), t_ccd)
-
-def _acq_success_prob(date, t_ccd, mag, color, spoiler, halfwidth):
-    out = acq_success_prob(date.decode(), float(t_ccd), float(mag), float(color), spoiler, int(halfwidth))
-    return out.tolist()
-
-def _prob_n_acq(acq_probs):
-    n_acq_probs, n_or_fewer_probs = prob_n_acq(acq_probs)
-    return n_acq_probs.tolist(), n_or_fewer_probs.tolist()
-};
-
-
-sub make_figure_of_merit{
-    my $c;
-    my $self = shift;
-    return unless ($c = $self->find_command("MP_STARCAT"));
-    return unless (defined $self->{ccd_temp});
-
-    my @probs;
-    my %slot_probs;
-
-    my $t_ccd = $self->{ccd_temp};
-    my $prob_limit = 0.008;
-
-    my $date = $c->{date};
-
-    foreach my $i (1..16) {
-	if ($c->{"TYPE$i"} =~ /BOT|ACQ/) {
-	    my $mag = $c->{"GS_MAG$i"};
-            my @warnings = grep {/\[\s{0,1}$i\]/} (@{$self->{warn}}, @{$self->{yellow_warn}});
-            my $spoiler = grep(/Search spoiler/i, @warnings) ? 1 : 0;
-            my $color = $c->{"GS_BV$i"};
-            my $hw = $c->{"HALFW$i"};
-            my $star_prob = _acq_success_prob($date, $t_ccd, $mag, $color, $spoiler, $hw);
-	    push @probs, $star_prob;
-            $slot_probs{$c->{"IMNUM$i"}} = $star_prob;
-            $c->{"P_ACQ$i"} = $star_prob;
-	}
-    }
-    $self->{acq_probs} = \%slot_probs;
-
-    # Calculate the probability of acquiring n stars
-    my ($n_acq_probs, $n_or_fewer_probs) = _prob_n_acq(\@probs);
-
-    $self->{figure_of_merit} = {expected => substr(sum(@probs), 0, 4),
-                                cum_prob => [map { log($_) / log(10.0) } @{$n_or_fewer_probs}],
-                                cum_prob_bad => ($n_or_fewer_probs->[2] > $prob_limit)
-                                };
-
-
-    if ($n_or_fewer_probs->[2] > $prob_limit){
-        push @{$self->{warn}}, ">> WARNING: Probability of 2 or fewer stars > $prob_limit\n";
-    }
-
-}
-
-
-sub set_dynamic_mag_limits{
-    my $c;
-    my $self = shift;
-    return unless ($c = $self->find_command("MP_STARCAT"));
-
-    my $date = $c->{date};
-    my $t_ccd = $self->{ccd_temp};
-    # Dynamic mag limits based on 75% and 50% chance of successful star acq
-    # Maximum limits of 10.3 and 10.6
-    $self->{mag_faint_yellow} = min(10.3, _mag_for_p_acq(0.75, $date, $t_ccd));
-    $self->{mag_faint_red} = min(10.6, _mag_for_p_acq(0.5, $date, $t_ccd));
-}
-
diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 64d9e2f9..83af1e4d 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -72,7 +72,7 @@ def _get_agasc_stars(ra, dec, roll, radius, date, agasc_file):
 };
 
 
-use List::Util qw(max min);
+use List::Util qw(min max);
 use Quat;
 use Ska::ACACoordConvert;
 use File::Basename;
@@ -81,7 +81,6 @@ use English;
 use IO::All;
 use Ska::Convert qw(date2time time2date);
 
-use Ska::Starcheck::FigureOfMerit qw( make_figure_of_merit set_dynamic_mag_limits );
 use RDB;
 
 use SQL::Abstract;
@@ -2178,14 +2177,10 @@ sub print_report {
     $o .= "\n";
 
     if (exists $self->{figure_of_merit}) {
-	my @probs = @{ $self->{figure_of_merit}->{cum_prob}};
 	my $bad_FOM = $self->{figure_of_merit}->{cum_prob_bad};
 	$o .= "$red_font_start" if $bad_FOM;
-	$o .= "Probability of acquiring 2,3, and 4 or fewer stars (10^x):\t";
-        # override formatting to match pre-JSON strings
-        foreach (2..4) {
-            $o .= substr(sprintf("%.4f", "$probs[$_]"), 0, 6) . "\t";
-        }
+	$o .= "Probability of acquiring 2 or fewer stars (10^x):\t";
+        $o .= substr(sprintf("%.4f", $self->{figure_of_merit}->{cum_prob_2}), 0, 6) . "\t";
 	$o .= "$font_stop" if $bad_FOM;
 	$o .= "\n";
 	$o .= sprintf("Acquisition Stars Expected  : %.2f\n",
@@ -2686,14 +2681,192 @@ sub set_ccd_temps{
         push @{$self->{warn}}, sprintf("$alarm Using %s (planning limit) for t_ccd for mag limits\n",
                                        $config{ccd_temp_red_limit});
         $self->{ccd_temp} = $config{ccd_temp_red_limit};
+        $self->{ccd_temp_acq} = $config{ccd_temp_red_limit};
         return;
     }
     # set the temperature to the value for the current obsid
     $self->{ccd_temp} = $obsid_temps->{$self->{obsid}}->{ccd_temp};
+    $self->{ccd_temp_acq} = $obsid_temps->{$self->{obsid}}->{ccd_temp_acq};
     $self->{n100_warm_frac} = $obsid_temps->{$self->{obsid}}->{n100_warm_frac};
     # add warnings for limit violations
     if ($self->{ccd_temp} > $config{ccd_temp_red_limit}){
         push @{$self->{fyi}}, sprintf("$info CCD temperature exceeds %.1f C\n",
                                        $config{ccd_temp_red_limit});
     }
+    if (($self->{ccd_temp_acq} > -1.0) or ($self->{ccd_temp_acq} < -16.0)){
+        push @{$self->{yellow_warn}}, sprintf(
+            ">> WARNING: acq t_ccd %.2f outside range -16.0 to -1.0. Clipped.",
+            $self->{ccd_temp_acq});
+        $self->{ccd_temp_acq} = $self->{ccd_temp_acq}  >  -1.0  ? -1.0
+                              : $self->{ccd_temp_acq}  < -16.0  ? -16.0
+                              : $self->{ccd_temp_acq};
+    }
+}
+
+use Inline Python => q{
+
+from proseco.acq import get_acq_catalog
+
+def calc_man_ang(q1, q2, q3, q4, initq1, initq2, initq3, initq4):
+    init_q = Quaternion.Quat([float(initq1), float(initq2), float(initq3), float(initq4)])
+    final_q = Quaternion.Quat([float(q1), float(q2), float(q3), float(q4)])
+    ang = float(np.degrees(2 * np.arccos(np.dot(init_q.q, final_q.q))))
+    ang = ang if ang <= 180 else 360 - ang
+    return ang
+
+
+def proseco_probs(kwargs):
+
+    kw = de_bytestr(kwargs)
+    acq_cat = get_acq_catalog(obsid=0, att=Quaternion.normalize([kw['q1'], kw['q2'], kw['q3'], kw['q4']]),
+                             n_acq=len(kw['acqs']), man_angle=kw['man_angle'], t_ccd=kw['t_ccd_acq'],
+                             date=kw['date'], dither=(kw['dither_acq_y'], kw['dither_acq_z']),
+                             detector=kw['detector'], sim_offset=kw['offset'],
+                             include_ids=kw['acqs'], include_halfws=kw['halfwidths'])
+    p_acqs = []
+    for acq in kw['acqs']:
+        if np.any(acq_cat['id'] == acq):
+            p_acqs.append(float(acq_cat['p_acq'][acq_cat['id'] == acq][0]))
+        else:
+            p_acqs.append(float(0.0))
+
+    return p_acqs, float(acq_cat.get_log_p_2_or_fewer()), float(np.sum(p_acqs))
+};
+
+
+
+sub proseco_args{
+
+    my $self = shift;
+    my %proseco_args;
+    my $targ_cmd = find_command($self, "MP_TARGQUAT");
+    my $cat_cmd = find_command($self, "MP_STARCAT");
+    if ((not $targ_cmd) or (not $cat_cmd)){
+        return \%proseco_args;
+    }
+    my $si = 'ACIS-S';
+    my $offset = 0;
+    if ($self->{obsid} < 38000){
+        $si = $self->{SI};
+        $offset = $self->{SIM_OFFSET_Z};
+    }
+    my $man_ang;
+    if (defined $targ_cmd->{initq1}){
+        $man_ang = calc_man_ang(
+            0 + $targ_cmd->{q1}, 0 + $targ_cmd->{q2},
+            0 + $targ_cmd->{q3}, 0 + $targ_cmd->{q4},
+            0 + $targ_cmd->{initq1}, 0 + $targ_cmd->{initq2},
+            0 + $targ_cmd->{initq3}, 0 + $targ_cmd->{initq4});
+    }
+
+    my @acq_ids;
+    my @acq_indexes;
+    my @gui_ids;
+    my @fid_ids;
+    my @halfwidths;
+    foreach my $i (1..16) {
+        if ($cat_cmd->{"TYPE$i"} =~ /BOT|ACQ/){
+            push @acq_ids, $cat_cmd->{"GS_ID$i"};
+            my $hw = $cat_cmd->{"HALFW$i"};
+            if (($hw > 180) or ($hw < 60)){
+                push @{$self->{yellow_warn}}, sprintf(
+                    ">> WARNING: [%2d] Halfwidth %d outside range 60 to 180. Clipped for probs.",
+                    $i, $hw);
+                # Clip hw if outside the range 60 to 180 for probabilities
+                $hw =   $hw < 60  ? 60
+                      : $hw > 180 ? 180
+                      : $hw ;
+            }
+            push @halfwidths, $hw;
+            push @acq_indexes, $i;
+        }
+        if ($cat_cmd->{"TYPE$i"} =~ /BOT|GUI/){
+            push @gui_ids, $cat_cmd->{"GS_ID$i"};
+        }
+        if ($cat_cmd->{"TYPE$i"} =~ /FID/){
+            push @fid_ids, $cat_cmd->{"GS_ID$i"};
+        }
+    }
+
+    %proseco_args = (
+        obsid => $self->{obsid},
+        date => $targ_cmd->{stop_date},
+        q1 => 0 + $targ_cmd->{q1}, q2 => 0 + $targ_cmd->{q2}, q3 => 0 + $targ_cmd->{q3}, q4 =>0 + $targ_cmd->{q4},
+        man_angle => $man_ang,
+        detector => $si, offset=> 0 + $offset,
+        dither_acq_y => $self->{dither_acq}->{ampl_y},
+        dither_acq_z => $self->{dither_acq}->{ampl_p},
+        dither_guide_y => $self->{dither_guide}->{ampl_y},
+        dither_guide_z => $self->{dither_guide}->{ampl_p},
+        t_ccd_acq => $self->{ccd_temp_acq},
+        t_ccd_guide => $self->{ccd_temp},
+        acqs => \@acq_ids,
+        halfwidths => \@halfwidths,
+        fids => \@fid_ids,
+        guides => \@gui_ids,
+        acq_indexes => \@acq_indexes);
+
+    return \%proseco_args
+
+}
+
+my $CUM_PROB_LIMIT = 0.008;
+
+sub set_proseco_probs{
+    my $self = shift;
+    my $cat_cmd = find_command($self, "MP_STARCAT");
+    my $args = $self->{proseco_args};
+    if ((not $cat_cmd)){
+        return
+    }
+    my ($p_acqs, $two_or_fewer, $expected) = proseco_probs($args);
+
+    my @acq_indexes = @{$args->{acq_indexes}};
+
+    # Assign those p_acqs to a slot hash and the catalog P_ACQ by index
+    my %slot_probs;
+    for my $idx (0 .. $#acq_indexes) {
+        my $i = $acq_indexes[$idx];
+        $cat_cmd->{"P_ACQ$i"} = $p_acqs->[$idx];
+        $slot_probs{$cat_cmd->{"IMNUM$i"}} = $p_acqs->[$idx];
+    }
+
+    $self->{acq_probs} = \%slot_probs;
+
+    $self->{figure_of_merit} = {expected => substr($expected, 0, 4),
+                                cum_prob_2 => $two_or_fewer,
+                                cum_prob_bad => ($two_or_fewer > $CUM_PROB_LIMIT)};
+    if ($two_or_fewer > $CUM_PROB_LIMIT){
+        push @{$self->{warn}}, ">> WARNING: Probability of 2 or fewer stars > $CUM_PROB_LIMIT\n";
+    }
+
+
+
+};
+
+
+
+use Inline Python => q{
+
+from chandra_aca.star_probs import mag_for_p_acq
+
+def _mag_for_p_acq(p_acq, date, t_ccd):
+    return mag_for_p_acq(p_acq, date.decode(), t_ccd)
+
+};
+
+
+
+sub set_dynamic_mag_limits{
+    my $c;
+    my $self = shift;
+    return unless ($c = $self->find_command("MP_STARCAT"));
+
+    my $date = $c->{date};
+    my $t_ccd = $self->{ccd_temp};
+    # Dynamic mag limits based on 75% and 50% chance of successful star acq
+    # Maximum limits of 10.3 and 10.6
+    $self->{mag_faint_yellow} = min(10.3, _mag_for_p_acq(0.75, $date, $t_ccd));
+    $self->{mag_faint_red} = min(10.6, _mag_for_p_acq(0.5, $date, $t_ccd));
 }
+
diff --git a/starcheck/src/starcheck.pl b/starcheck/src/starcheck.pl
index 1b450c96..25c974d8 100755
--- a/starcheck/src/starcheck.pl
+++ b/starcheck/src/starcheck.pl
@@ -644,7 +644,10 @@ sub json_obsids{
     if ($bs[0]->{time} > date2time('2017:043:00:00:00.000')){
         $obs{$obsid}->check_big_box_stars();
     }
-    $obs{$obsid}->make_figure_of_merit();
+    # Get the args that proseco would want
+    $obs{$obsid}->{'proseco_args'} = $obs{$obsid}->proseco_args();
+    $obs{$obsid}->set_proseco_probs();
+
 # Make sure there is only one star catalog per obsid
     warning ("More than one star catalog assigned to Obsid $obsid\n")
 	if ($obs{$obsid}->find_command('MP_STARCAT',2));

From 003cdc696d32800ca0b55c59c223715c1cbd5a19 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 7 Jan 2019 14:13:02 -0500
Subject: [PATCH 03/23] Remove FigureOfMerit from Makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index fb7bb105..1c94a8f9 100644
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,7 @@ SRC = starcheck/src
 
 RELATED_LIB = $(SRC)/StarcheckParser.pm
 BIN = $(SRC)/starcheck.pl $(SRC)/starcheck
-LIB = $(SRC)/lib/Ska/Starcheck/Obsid.pm $(SRC)/lib/Ska/Starcheck/FigureOfMerit.pm \
+LIB = $(SRC)/lib/Ska/Starcheck/Obsid.pm \
 	$(SRC)/lib/Ska/Starcheck/Dark_Cal_Checker.pm $(SRC)/lib/Ska/Parse_CM_File.pm
 PYTHON_LIB = starcheck/calc_ccd_temps.py starcheck/pcad_att_check.py starcheck/plot.py \
              starcheck/version.py starcheck/__init__.py

From 4be5b72d27683cb1d1eaac11aa53e40df101ef0c Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 7 Jan 2019 14:14:15 -0500
Subject: [PATCH 04/23] Use maneuver summary maneuver angle instead of
 calculating it

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 17 +++--------------
 1 file changed, 3 insertions(+), 14 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 83af1e4d..197edaa6 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2707,13 +2707,6 @@ use Inline Python => q{
 
 from proseco.acq import get_acq_catalog
 
-def calc_man_ang(q1, q2, q3, q4, initq1, initq2, initq3, initq4):
-    init_q = Quaternion.Quat([float(initq1), float(initq2), float(initq3), float(initq4)])
-    final_q = Quaternion.Quat([float(q1), float(q2), float(q3), float(q4)])
-    ang = float(np.degrees(2 * np.arccos(np.dot(init_q.q, final_q.q))))
-    ang = ang if ang <= 180 else 360 - ang
-    return ang
-
 
 def proseco_probs(kwargs):
 
@@ -2750,13 +2743,9 @@ sub proseco_args{
         $si = $self->{SI};
         $offset = $self->{SIM_OFFSET_Z};
     }
-    my $man_ang;
-    if (defined $targ_cmd->{initq1}){
-        $man_ang = calc_man_ang(
-            0 + $targ_cmd->{q1}, 0 + $targ_cmd->{q2},
-            0 + $targ_cmd->{q3}, 0 + $targ_cmd->{q4},
-            0 + $targ_cmd->{initq1}, 0 + $targ_cmd->{initq2},
-            0 + $targ_cmd->{initq3}, 0 + $targ_cmd->{initq4});
+    my $man_ang = 90;
+    if (defined $targ_cmd->{angle}){
+        $man_ang = $targ_cmd->{angle};
     }
 
     my @acq_ids;

From 911d4a3831eab45aed217cb67a5a35f1ce5eebe2 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 7 Jan 2019 14:15:35 -0500
Subject: [PATCH 05/23] Handle missing data (ReOpen schedule beginning) for
 proseco probs

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 42 +++++++++++++++++-------
 1 file changed, 30 insertions(+), 12 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 197edaa6..97af5451 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2027,9 +2027,13 @@ sub print_report {
 
             my $acq_prob = "";
             if ($c->{"TYPE$i"} =~ /BOT|ACQ/){
-                my $prob = $self->{acq_probs}->{$c->{"IMNUM${i}"}};
-                $acq_prob = sprintf("Prob Acq Success %5.3f", $prob);
-
+                if (defined $self->{acq_probs}->{$c->{"IMNUM${i}"}}){
+                    my $prob = $self->{acq_probs}->{$c->{"IMNUM${i}"}};
+                    $acq_prob = sprintf("Prob Acq Success %5.3f", $prob);
+                }
+                else{
+                    $acq_prob = sprintf("Prob Acq Success 0.0");
+                }
             }
             # Make the id a URL if there is star history or if star history could
             # not be checked (no db_handle)
@@ -2753,9 +2757,25 @@ sub proseco_args{
     my @gui_ids;
     my @fid_ids;
     my @halfwidths;
+  IDX:
     foreach my $i (1..16) {
+        (my $sid  = $cat_cmd->{"GS_ID$i"}) =~ s/[\s\*]//g;
+        # If there is no star there is nothing for proseco probs to do so skip it.
+        # But warn if it was a thing that should have had an id (BOT/ACQ/GUI).
+        if ($sid eq '---'){
+            if ($cat_cmd->{"TYPE$i"} =~ /BOT|ACQ|GUI/){
+                push @{$self->{warn}}, sprintf(
+                    ">> WARNING: [%2d] Could not calculate acq prob for star with no id.", $i);
+            }
+            next IDX;
+        }
+        $sid = int($sid);
+        ## Strip off asterisk if present (there's probably a cleaner Perl way to do this).
+        #if ($sid =~ /\*(\d+)/){
+        #    $sid = $1;
+        #}
         if ($cat_cmd->{"TYPE$i"} =~ /BOT|ACQ/){
-            push @acq_ids, $cat_cmd->{"GS_ID$i"};
+            push @acq_ids, $sid;;
             my $hw = $cat_cmd->{"HALFW$i"};
             if (($hw > 180) or ($hw < 60)){
                 push @{$self->{yellow_warn}}, sprintf(
@@ -2770,10 +2790,10 @@ sub proseco_args{
             push @acq_indexes, $i;
         }
         if ($cat_cmd->{"TYPE$i"} =~ /BOT|GUI/){
-            push @gui_ids, $cat_cmd->{"GS_ID$i"};
+            push @gui_ids, $sid;
         }
         if ($cat_cmd->{"TYPE$i"} =~ /FID/){
-            push @fid_ids, $cat_cmd->{"GS_ID$i"};
+            push @fid_ids, $sid;
         }
     }
 
@@ -2805,8 +2825,9 @@ sub set_proseco_probs{
     my $self = shift;
     my $cat_cmd = find_command($self, "MP_STARCAT");
     my $args = $self->{proseco_args};
-    if ((not $cat_cmd)){
-        return
+
+    if (not %{$args}){
+        return;
     }
     my ($p_acqs, $two_or_fewer, $expected) = proseco_probs($args);
 
@@ -2828,10 +2849,7 @@ sub set_proseco_probs{
     if ($two_or_fewer > $CUM_PROB_LIMIT){
         push @{$self->{warn}}, ">> WARNING: Probability of 2 or fewer stars > $CUM_PROB_LIMIT\n";
     }
-
-
-
-};
+}
 
 
 

From a1e2276c847a12c2a2490414c13e2a15b4453f6c Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 7 Jan 2019 14:16:40 -0500
Subject: [PATCH 06/23] Use the 'last' maneuver for maneuver angle (for
 segmented manvrs for now)

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 97af5451..e61b4edc 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2736,7 +2736,7 @@ sub proseco_args{
 
     my $self = shift;
     my %proseco_args;
-    my $targ_cmd = find_command($self, "MP_TARGQUAT");
+    my $targ_cmd = find_command($self, "MP_TARGQUAT", -1);
     my $cat_cmd = find_command($self, "MP_STARCAT");
     if ((not $targ_cmd) or (not $cat_cmd)){
         return \%proseco_args;

From 0e75f3fd378af8ced81dd3bad3abc7d7eb81dce1 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 7 Jan 2019 14:17:05 -0500
Subject: [PATCH 07/23] Skip trying for proseco args for NONE obsids

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index e61b4edc..a6b0f194 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2738,7 +2738,7 @@ sub proseco_args{
     my %proseco_args;
     my $targ_cmd = find_command($self, "MP_TARGQUAT", -1);
     my $cat_cmd = find_command($self, "MP_STARCAT");
-    if ((not $targ_cmd) or (not $cat_cmd)){
+    if ((not $targ_cmd) or (not $cat_cmd) or ($self->{obsid} =~ /NONE(\d+)/)){
         return \%proseco_args;
     }
     my $si = 'ACIS-S';

From 887e7bfba140e16e3bfaddaaca87548a1d4f76d8 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 7 Jan 2019 14:43:36 -0500
Subject: [PATCH 08/23] Recharacterize big box warning as yellow_warn

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index a6b0f194..43fb5f71 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2668,7 +2668,7 @@ sub check_big_box_stars{
         }
     }
     if ($big_box_count < 3){
-        push @{$self->{warn}}, "$alarm Fewer than 3 ACQ stars with boxes >= 160 arcsec\n";
+        push @{$self->{yellow_warn}}, "$alarm Fewer than 3 ACQ stars with boxes >= 160 arcsec\n";
     }
 }
 

From 98dc5bded57ab10a5ae5116cfdaf69a249b3d6f2 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:34:05 -0500
Subject: [PATCH 09/23] Add comment for empty hover-over acq prob and simplify
 a bit

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 43fb5f71..cd7ffb66 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2024,15 +2024,15 @@ sub print_report {
 		$idpad_n --;
 	    }
 
-
+            # Get a string for acquisition probability in the hover-over
             my $acq_prob = "";
             if ($c->{"TYPE$i"} =~ /BOT|ACQ/){
+                # Fetch this slot's acq probability for the hover-over string,
+                # but if the probability is not defined (expected for weird cases such as
+                # replan/reopen) just leave $acq_prob as the initialized empty string.
                 if (defined $self->{acq_probs}->{$c->{"IMNUM${i}"}}){
-                    my $prob = $self->{acq_probs}->{$c->{"IMNUM${i}"}};
-                    $acq_prob = sprintf("Prob Acq Success %5.3f", $prob);
-                }
-                else{
-                    $acq_prob = sprintf("Prob Acq Success 0.0");
+                    $acq_prob = sprintf("Prob Acq Success %5.3f",
+                                        $self->{acq_probs}->{$c->{"IMNUM${i}"}})
                 }
             }
             # Make the id a URL if there is star history or if star history could

From 2082c6d19966ac8324e0fc2d0108bca5b871dc5b Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:35:21 -0500
Subject: [PATCH 10/23] Remove big box check and set proseco probs earlier in
 loop in starcheck.pl

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 21 ---------------------
 starcheck/src/starcheck.pl               | 10 +++-------
 2 files changed, 3 insertions(+), 28 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index cd7ffb66..2a77e6ed 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2651,27 +2651,6 @@ sub count_guide_stars{
     return _guide_count(\@mags, $self->{ccd_temp});
 }
 
-###################################################################################
-sub check_big_box_stars{
-###################################################################################
-    my $self = shift;
-    my $c;
-    my $big_box_count = 0;
-    return unless ($c = find_command($self, 'MP_STARCAT'));
-    for my $i (1 .. 16){
-        my $type = $c->{"TYPE$i"};
-        my $hw = $c->{"HALFW$i"};
-        if ($type =~ /ACQ|BOT/){
-            if ($hw >= 160){
-                $big_box_count++;
-            }
-        }
-    }
-    if ($big_box_count < 3){
-        push @{$self->{yellow_warn}}, "$alarm Fewer than 3 ACQ stars with boxes >= 160 arcsec\n";
-    }
-}
-
 
 ###################################################################################
 sub set_ccd_temps{
diff --git a/starcheck/src/starcheck.pl b/starcheck/src/starcheck.pl
index 25c974d8..1caf3a3a 100755
--- a/starcheck/src/starcheck.pl
+++ b/starcheck/src/starcheck.pl
@@ -635,18 +635,14 @@ sub json_obsids{
     $obs{$obsid}->check_flick_pix_mon();
     $obs{$obsid}->set_dynamic_mag_limits();
     $obs{$obsid}->check_dither($dither);
+    # Get the args that proseco would want
+    $obs{$obsid}->{'proseco_args'} = $obs{$obsid}->proseco_args();
+    $obs{$obsid}->set_proseco_probs();
     $obs{$obsid}->check_star_catalog($or{$obsid}, $par{vehicle});
     $obs{$obsid}->check_sim_position(@sim_trans) unless $par{vehicle};
 	$obs{$obsid}->check_momentum_unload(\@bs);
     $obs{$obsid}->check_for_special_case_er();
     $obs{$obsid}->check_bright_perigee($radmon);
-    # Start check for big boxes at FEB1317 (which gets test products but no regress products)
-    if ($bs[0]->{time} > date2time('2017:043:00:00:00.000')){
-        $obs{$obsid}->check_big_box_stars();
-    }
-    # Get the args that proseco would want
-    $obs{$obsid}->{'proseco_args'} = $obs{$obsid}->proseco_args();
-    $obs{$obsid}->set_proseco_probs();
 
 # Make sure there is only one star catalog per obsid
     warning ("More than one star catalog assigned to Obsid $obsid\n")

From 998ff4660e8e4f23833b4bab20af5ceaee03e892 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:51:50 -0500
Subject: [PATCH 11/23] Assume the best

This change sets proseco_probs to assume that the supplied acq ids all
have appropriate acq probs.  It also assumes that a manuever angle
is set for each observations.
---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 15 ++++-----------
 1 file changed, 4 insertions(+), 11 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 2a77e6ed..cc989d87 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2699,12 +2699,9 @@ def proseco_probs(kwargs):
                              date=kw['date'], dither=(kw['dither_acq_y'], kw['dither_acq_z']),
                              detector=kw['detector'], sim_offset=kw['offset'],
                              include_ids=kw['acqs'], include_halfws=kw['halfwidths'])
-    p_acqs = []
-    for acq in kw['acqs']:
-        if np.any(acq_cat['id'] == acq):
-            p_acqs.append(float(acq_cat['p_acq'][acq_cat['id'] == acq][0]))
-        else:
-            p_acqs.append(float(0.0))
+
+    # Assign the proseco probabilities back into an array.
+    p_acqs = [float(acq_cat['p_acq'][acq_cat['id'] == acq][0]) for acq in kw['acqs']]
 
     return p_acqs, float(acq_cat.get_log_p_2_or_fewer()), float(np.sum(p_acqs))
 };
@@ -2726,10 +2723,6 @@ sub proseco_args{
         $si = $self->{SI};
         $offset = $self->{SIM_OFFSET_Z};
     }
-    my $man_ang = 90;
-    if (defined $targ_cmd->{angle}){
-        $man_ang = $targ_cmd->{angle};
-    }
 
     my @acq_ids;
     my @acq_indexes;
@@ -2780,7 +2773,7 @@ sub proseco_args{
         obsid => $self->{obsid},
         date => $targ_cmd->{stop_date},
         q1 => 0 + $targ_cmd->{q1}, q2 => 0 + $targ_cmd->{q2}, q3 => 0 + $targ_cmd->{q3}, q4 =>0 + $targ_cmd->{q4},
-        man_angle => $man_ang,
+        man_angle => 0 + $targ_cmd->{angle},
         detector => $si, offset=> 0 + $offset,
         dither_acq_y => $self->{dither_acq}->{ampl_y},
         dither_acq_z => $self->{dither_acq}->{ampl_p},

From a01658b9940b69e449c1ade125edb2548fbe9605 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:55:54 -0500
Subject: [PATCH 12/23] Update comments/docstrings (and fiddle with whitespace)

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 65 ++++++++++++++++++++----
 1 file changed, 55 insertions(+), 10 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index cc989d87..57408a50 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2690,8 +2690,30 @@ use Inline Python => q{
 
 from proseco.acq import get_acq_catalog
 
-
 def proseco_probs(kwargs):
+    """
+    Call proseco's get_acq_catalog with the parameters supplied in `kwargs` for a specific obsid catalog
+    and return the individual acq star probabilities, the P2 value for the catalog, and the expected
+    number of acq stars.
+
+    `kwargs` will be a Perl hash converted to dict (by Inline) of the expected keyword params. These keys
+    must be defined:
+
+    'q1', 'q2', 'q3', 'q4' = the target quaternion
+    'man_angle' the maneuver angle to the target quaternion in degrees.
+    'acqs' list of acq star ids
+    'halfwidths' list of acq star halfwidths in arcsecs
+    't_ccd_acq' acquisition temperature in deg C
+    'date' observation date (in Chandra.Time compatible format)
+    'detector' science detector
+    'sim_offset' SIM offset
+
+    As these values are from a Perl hash, bytestrings will be converted by de_bytestr early in this method.
+
+    :param kwargs: dict of expected keywords
+    :return tuple: (list of floats of star acq probabilties, float P2, float expected acq stars)
+
+    """
 
     kw = de_bytestr(kwargs)
     acq_cat = get_acq_catalog(obsid=0, att=Quaternion.normalize([kw['q1'], kw['q2'], kw['q3'], kw['q4']]),
@@ -2707,16 +2729,26 @@ def proseco_probs(kwargs):
 };
 
 
-
+###################################################################################
 sub proseco_args{
-
+###################################################################################
+# Build a hash that corresponds to reasonable arguments to use to call proseco get_acq_catalog
+# to calculate marginalized acquisition probabilities for a star catalog.
+# This routine also saves the guides and fids into lists, but those are not used
+# by get_acq_catalog.
+# If an observation does not have a target quaternion or a starcat, it is skipped and
+# an empty hash is returned with no warning.
     my $self = shift;
     my %proseco_args;
+    # For the target quaternion, use the -1 to get the last quaternion (there could be more than
+    # one for a segmented maneuver).
     my $targ_cmd = find_command($self, "MP_TARGQUAT", -1);
     my $cat_cmd = find_command($self, "MP_STARCAT");
+    # For observations without a target attitude, catalog, or defined obsid return an empty hash
     if ((not $targ_cmd) or (not $cat_cmd) or ($self->{obsid} =~ /NONE(\d+)/)){
         return \%proseco_args;
     }
+    # Use a default SI (which should only be used for ERs and should have no effect without fid lights)
     my $si = 'ACIS-S';
     my $offset = 0;
     if ($self->{obsid} < 38000){
@@ -2729,6 +2761,7 @@ sub proseco_args{
     my @gui_ids;
     my @fid_ids;
     my @halfwidths;
+    # Loop over the star catalog and assign the acqs, guide stars, and fids to arrays.
   IDX:
     foreach my $i (1..16) {
         (my $sid  = $cat_cmd->{"GS_ID$i"}) =~ s/[\s\*]//g;
@@ -2742,10 +2775,7 @@ sub proseco_args{
             next IDX;
         }
         $sid = int($sid);
-        ## Strip off asterisk if present (there's probably a cleaner Perl way to do this).
-        #if ($sid =~ /\*(\d+)/){
-        #    $sid = $1;
-        #}
+        # While assigning ACQ stars into a list, clip to allowed ranges and warn as needed.
         if ($cat_cmd->{"TYPE$i"} =~ /BOT|ACQ/){
             push @acq_ids, $sid;;
             my $hw = $cat_cmd->{"HALFW$i"};
@@ -2769,6 +2799,9 @@ sub proseco_args{
         }
     }
 
+    # Build a hash of the arguments that could be used by proseco (get_aca_catalog or get_acq_catalog).
+    # Zeros are added to most of the numeric parameters as that seems to help "cast" them to floats or ints in
+    # Perl to some extent.
     %proseco_args = (
         obsid => $self->{obsid},
         date => $targ_cmd->{stop_date},
@@ -2791,9 +2824,16 @@ sub proseco_args{
 
 }
 
-my $CUM_PROB_LIMIT = 0.008;
 
+###################################################################################
 sub set_proseco_probs{
+###################################################################################
+# For observations with a star catalog and which have valid parameters already determined
+# in $self->{proseco_args}, call the Python proseco_probs method to calculate the
+# marginalized probabilities, P2, and expected stars, and assign those values back
+# where expected in the data structure.
+# This assigns the individual acq star probabilites back into $self->{acq_probs} and
+# assigns the P2 and expected values into $self->{figure_of_merit}.
     my $self = shift;
     my $cat_cmd = find_command($self, "MP_STARCAT");
     my $args = $self->{proseco_args};
@@ -2812,7 +2852,6 @@ sub set_proseco_probs{
         $cat_cmd->{"P_ACQ$i"} = $p_acqs->[$idx];
         $slot_probs{$cat_cmd->{"IMNUM$i"}} = $p_acqs->[$idx];
     }
-
     $self->{acq_probs} = \%slot_probs;
 
     $self->{figure_of_merit} = {expected => substr($expected, 0, 4),
@@ -2830,13 +2869,19 @@ use Inline Python => q{
 from chandra_aca.star_probs import mag_for_p_acq
 
 def _mag_for_p_acq(p_acq, date, t_ccd):
-    return mag_for_p_acq(p_acq, date.decode(), t_ccd)
+    """
+    Call mag_for_p_acq, but cast p_acq and t_ccd as floats (may or may not be needed) and
+    convert date from a bytestring (from the Perl interface).
+    """
+    return mag_for_p_acq(float(p_acq), date.decode(), float(t_ccd))
 
 };
 
 
 
 sub set_dynamic_mag_limits{
+# Use the t_ccd at time of acquistion and time to set the mag limits corresponding to the the magnitude
+# for a 75% acquisition succes (yellow limit) and a 50% acquisition success (red limit)
     my $c;
     my $self = shift;
     return unless ($c = $self->find_command("MP_STARCAT"));

From c8a4bc04c38ced97488f53b6ef063114e89d1b8b Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:56:20 -0500
Subject: [PATCH 13/23] Set P2 to 2.0 and use more local variable

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 57408a50..348b367c 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2854,11 +2854,13 @@ sub set_proseco_probs{
     }
     $self->{acq_probs} = \%slot_probs;
 
+    # Set the P2 to be 2.0 (aka 0.01)
+    my $cum_prob_limit = 0.01;
     $self->{figure_of_merit} = {expected => substr($expected, 0, 4),
                                 cum_prob_2 => $two_or_fewer,
-                                cum_prob_bad => ($two_or_fewer > $CUM_PROB_LIMIT)};
-    if ($two_or_fewer > $CUM_PROB_LIMIT){
-        push @{$self->{warn}}, ">> WARNING: Probability of 2 or fewer stars > $CUM_PROB_LIMIT\n";
+                                cum_prob_bad => ($two_or_fewer > $cum_prob_limit)};
+    if ($two_or_fewer > $cum_prob_limit){
+        push @{$self->{warn}}, ">> WARNING: Probability of 2 or fewer stars > $cum_prob_limit\n";
     }
 }
 

From cb88ae606a18b39d1b57ddb1f481b7d942a80fdd Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:56:47 -0500
Subject: [PATCH 14/23] Use acq phase temperature for mag limits

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 348b367c..3bb32acb 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2889,7 +2889,7 @@ sub set_dynamic_mag_limits{
     return unless ($c = $self->find_command("MP_STARCAT"));
 
     my $date = $c->{date};
-    my $t_ccd = $self->{ccd_temp};
+    my $t_ccd = $self->{ccd_temp_acq};
     # Dynamic mag limits based on 75% and 50% chance of successful star acq
     # Maximum limits of 10.3 and 10.6
     $self->{mag_faint_yellow} = min(10.3, _mag_for_p_acq(0.75, $date, $t_ccd));

From 788a673be6318719a1e041d75f09cfef4eb4ba35 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Mon, 14 Jan 2019 16:57:48 -0500
Subject: [PATCH 15/23] Remove if statement setting acq temperature

---
 starcheck/calc_ccd_temps.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/starcheck/calc_ccd_temps.py b/starcheck/calc_ccd_temps.py
index c10cbbb5..bd7efbbe 100755
--- a/starcheck/calc_ccd_temps.py
+++ b/starcheck/calc_ccd_temps.py
@@ -210,7 +210,7 @@ def get_interval_data(intervals, times, ccd_temp, obsreqs=None):
             obstemps[str(interval['obsid'])] = obs
             continue
         obs['ccd_temp'] = np.max(ok_temps)
-        obs['ccd_temp_acq'] = np.max(ok_temps[0:2]) if len(ok_temps) > 1 else obs['ccd_temp']
+        obs['ccd_temp_acq'] = np.max(ok_temps[:2])
         obs['n100_warm_frac'] = dark_model.get_warm_fracs(
             100, interval['tstart'], np.max(ok_temps))
         # If we have an OR list, the obsid is in that list, and the OR list has zero-offset keys

From 44fc15e39adbda21b1e98aa8eff7aff72caa3328 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Tue, 15 Jan 2019 08:29:33 -0500
Subject: [PATCH 16/23] Remove halfwidth clipping and update comments and
 warning

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 3bb32acb..24b88196 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2775,18 +2775,15 @@ sub proseco_args{
             next IDX;
         }
         $sid = int($sid);
-        # While assigning ACQ stars into a list, clip to allowed ranges and warn as needed.
+        # While assigning ACQ stars into a list, warn if outside the 60 to 180 range used by proseco
+        # and the grid acq model.
         if ($cat_cmd->{"TYPE$i"} =~ /BOT|ACQ/){
             push @acq_ids, $sid;;
             my $hw = $cat_cmd->{"HALFW$i"};
             if (($hw > 180) or ($hw < 60)){
-                push @{$self->{yellow_warn}}, sprintf(
-                    ">> WARNING: [%2d] Halfwidth %d outside range 60 to 180. Clipped for probs.",
+                push @{$self->{orange_warn}}, sprintf(
+                    ">> WARNING: [%2d] Halfwidth %d outside range 60 to 180. Will be clipped in proseco probs.\n",
                     $i, $hw);
-                # Clip hw if outside the range 60 to 180 for probabilities
-                $hw =   $hw < 60  ? 60
-                      : $hw > 180 ? 180
-                      : $hw ;
             }
             push @halfwidths, $hw;
             push @acq_indexes, $i;

From b4656b1fae819cdfed64539f5d47013c3684b04b Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Tue, 15 Jan 2019 08:33:21 -0500
Subject: [PATCH 17/23] Add newline at end of acq ccd clip warn.

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 24b88196..94c9fda3 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2678,7 +2678,7 @@ sub set_ccd_temps{
     }
     if (($self->{ccd_temp_acq} > -1.0) or ($self->{ccd_temp_acq} < -16.0)){
         push @{$self->{yellow_warn}}, sprintf(
-            ">> WARNING: acq t_ccd %.2f outside range -16.0 to -1.0. Clipped.",
+            ">> WARNING: acq t_ccd %.2f outside range -16.0 to -1.0. Clipped.\n",
             $self->{ccd_temp_acq});
         $self->{ccd_temp_acq} = $self->{ccd_temp_acq}  >  -1.0  ? -1.0
                               : $self->{ccd_temp_acq}  < -16.0  ? -16.0

From cc897a1ae976a1bc6e79071b83ca392f840197f7 Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Tue, 15 Jan 2019 09:41:54 -0500
Subject: [PATCH 18/23] Set to be the right value for P2 and use P2
 consistently

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 94c9fda3..c44373ff 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2183,8 +2183,8 @@ sub print_report {
     if (exists $self->{figure_of_merit}) {
 	my $bad_FOM = $self->{figure_of_merit}->{cum_prob_bad};
 	$o .= "$red_font_start" if $bad_FOM;
-	$o .= "Probability of acquiring 2 or fewer stars (10^x):\t";
-        $o .= substr(sprintf("%.4f", $self->{figure_of_merit}->{cum_prob_2}), 0, 6) . "\t";
+	$o .= "Probability of acquiring 2 or fewer stars (10^-x):\t";
+        $o .= substr(sprintf("%.4f", $self->{figure_of_merit}->{P2}), 0, 6) . "\t";
 	$o .= "$font_stop" if $bad_FOM;
 	$o .= "\n";
 	$o .= sprintf("Acquisition Stars Expected  : %.2f\n",
@@ -2725,7 +2725,7 @@ def proseco_probs(kwargs):
     # Assign the proseco probabilities back into an array.
     p_acqs = [float(acq_cat['p_acq'][acq_cat['id'] == acq][0]) for acq in kw['acqs']]
 
-    return p_acqs, float(acq_cat.get_log_p_2_or_fewer()), float(np.sum(p_acqs))
+    return p_acqs, float(-np.log10(acq_cat.calc_p_safe())), float(np.sum(p_acqs))
 };
 
 
@@ -2838,7 +2838,7 @@ sub set_proseco_probs{
     if (not %{$args}){
         return;
     }
-    my ($p_acqs, $two_or_fewer, $expected) = proseco_probs($args);
+    my ($p_acqs, $P2, $expected) = proseco_probs($args);
 
     my @acq_indexes = @{$args->{acq_indexes}};
 
@@ -2851,13 +2851,13 @@ sub set_proseco_probs{
     }
     $self->{acq_probs} = \%slot_probs;
 
-    # Set the P2 to be 2.0 (aka 0.01)
-    my $cum_prob_limit = 0.01;
+    # Set the P2 requirement to be 2.0
+    my $P2_required = 2.0;
     $self->{figure_of_merit} = {expected => substr($expected, 0, 4),
-                                cum_prob_2 => $two_or_fewer,
-                                cum_prob_bad => ($two_or_fewer > $cum_prob_limit)};
-    if ($two_or_fewer > $cum_prob_limit){
-        push @{$self->{warn}}, ">> WARNING: Probability of 2 or fewer stars > $cum_prob_limit\n";
+                                P2 => $P2,
+                                cum_prob_bad => ($P2 < $P2_required)};
+    if ($P2 < $P2_required){
+        push @{$self->{warn}}, ">> WARNING: -log10 probability of 2 or fewer stars < $P2_required\n";
     }
 }
 

From 33bd6e49df49f9804a9d415f76baf4b839b51bdd Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Tue, 15 Jan 2019 09:50:53 -0500
Subject: [PATCH 19/23] Use less ambiguous keys in the proseco arg hash

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index c44373ff..b4aa7e05 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2701,7 +2701,7 @@ def proseco_probs(kwargs):
 
     'q1', 'q2', 'q3', 'q4' = the target quaternion
     'man_angle' the maneuver angle to the target quaternion in degrees.
-    'acqs' list of acq star ids
+    'acq_ids' list of acq star ids
     'halfwidths' list of acq star halfwidths in arcsecs
     't_ccd_acq' acquisition temperature in deg C
     'date' observation date (in Chandra.Time compatible format)
@@ -2717,13 +2717,13 @@ def proseco_probs(kwargs):
 
     kw = de_bytestr(kwargs)
     acq_cat = get_acq_catalog(obsid=0, att=Quaternion.normalize([kw['q1'], kw['q2'], kw['q3'], kw['q4']]),
-                             n_acq=len(kw['acqs']), man_angle=kw['man_angle'], t_ccd=kw['t_ccd_acq'],
+                             n_acq=len(kw['acq_ids']), man_angle=kw['man_angle'], t_ccd=kw['t_ccd_acq'],
                              date=kw['date'], dither=(kw['dither_acq_y'], kw['dither_acq_z']),
                              detector=kw['detector'], sim_offset=kw['offset'],
-                             include_ids=kw['acqs'], include_halfws=kw['halfwidths'])
+                             include_ids=kw['acq_ids'], include_halfws=kw['halfwidths'])
 
     # Assign the proseco probabilities back into an array.
-    p_acqs = [float(acq_cat['p_acq'][acq_cat['id'] == acq][0]) for acq in kw['acqs']]
+    p_acqs = [float(acq_cat['p_acq'][acq_cat['id'] == acq_id][0]) for acq_id in kw['acq_ids']]
 
     return p_acqs, float(-np.log10(acq_cat.calc_p_safe())), float(np.sum(p_acqs))
 };
@@ -2761,7 +2761,7 @@ sub proseco_args{
     my @gui_ids;
     my @fid_ids;
     my @halfwidths;
-    # Loop over the star catalog and assign the acqs, guide stars, and fids to arrays.
+    # Loop over the star catalog and assign the acq stars, guide stars, and fids to arrays.
   IDX:
     foreach my $i (1..16) {
         (my $sid  = $cat_cmd->{"GS_ID$i"}) =~ s/[\s\*]//g;
@@ -2798,7 +2798,8 @@ sub proseco_args{
 
     # Build a hash of the arguments that could be used by proseco (get_aca_catalog or get_acq_catalog).
     # Zeros are added to most of the numeric parameters as that seems to help "cast" them to floats or ints in
-    # Perl to some extent.
+    # Perl to some extent.  Also save the acquisition star catalog indexes to make it easier to assign back
+    # the probabilities without having to search again on the Perl side by agasc id.
     %proseco_args = (
         obsid => $self->{obsid},
         date => $targ_cmd->{stop_date},
@@ -2811,10 +2812,10 @@ sub proseco_args{
         dither_guide_z => $self->{dither_guide}->{ampl_p},
         t_ccd_acq => $self->{ccd_temp_acq},
         t_ccd_guide => $self->{ccd_temp},
-        acqs => \@acq_ids,
+        acq_ids => \@acq_ids,
         halfwidths => \@halfwidths,
-        fids => \@fid_ids,
-        guides => \@gui_ids,
+        fid_ids => \@fid_ids,
+        guide_ids => \@gui_ids,
         acq_indexes => \@acq_indexes);
 
     return \%proseco_args

From 473a313644abd6636a194134f99de4d7908fb47c Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Tue, 15 Jan 2019 09:54:36 -0500
Subject: [PATCH 20/23] Add comment to temperature clipping

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index b4aa7e05..c2609566 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2676,6 +2676,8 @@ sub set_ccd_temps{
         push @{$self->{fyi}}, sprintf("$info CCD temperature exceeds %.1f C\n",
                                        $config{ccd_temp_red_limit});
     }
+    # Clip the acq ccd temperature to the calibrated range of the grid acq probability model
+    # and add a yellow warning to let the user know this has happened.
     if (($self->{ccd_temp_acq} > -1.0) or ($self->{ccd_temp_acq} < -16.0)){
         push @{$self->{yellow_warn}}, sprintf(
             ">> WARNING: acq t_ccd %.2f outside range -16.0 to -1.0. Clipped.\n",

From 78e19bddc408b4dc8a7e7a310417dec9304168be Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Tue, 15 Jan 2019 09:58:48 -0500
Subject: [PATCH 21/23] Use ternary to set SI and SIM_OFFSET_Z for proseco

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index c2609566..44419c8f 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2750,13 +2750,10 @@ sub proseco_args{
     if ((not $targ_cmd) or (not $cat_cmd) or ($self->{obsid} =~ /NONE(\d+)/)){
         return \%proseco_args;
     }
-    # Use a default SI (which should only be used for ERs and should have no effect without fid lights)
-    my $si = 'ACIS-S';
-    my $offset = 0;
-    if ($self->{obsid} < 38000){
-        $si = $self->{SI};
-        $offset = $self->{SIM_OFFSET_Z};
-    }
+    # Use a default SI and offset for ERs (no effect without fid lights)
+    my $is_OR = $self->{obsid} < $ER_MIN_OBSID;
+    my $si = $is_OR ? $self->{SI} : 'ACIS-S';
+    my $offset = $is_OR ? $self->{SIM_OFFSET_Z} : 0;
 
     my @acq_ids;
     my @acq_indexes;

From 945fa198e5c43d337d1a475743d1a96f1be2f8ca Mon Sep 17 00:00:00 2001
From: Jean Connelly <jconnelly@cfa.harvard.edu>
Date: Wed, 16 Jan 2019 21:00:45 -0500
Subject: [PATCH 22/23] Set more conservative P2 of 3.0 for ERs and to use as
 yellow-warn for ORs

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 44419c8f..39b979d9 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2851,14 +2851,20 @@ sub set_proseco_probs{
     }
     $self->{acq_probs} = \%slot_probs;
 
-    # Set the P2 requirement to be 2.0
-    my $P2_required = 2.0;
+    # Set the P2 requirement to be 2.0 for ORs and 3.0 for ERs.
+    my $P2_required = $self->{obsid} < $ER_MIN_OBSID ? 2.0 : 3.0;
     $self->{figure_of_merit} = {expected => substr($expected, 0, 4),
                                 P2 => $P2,
                                 cum_prob_bad => ($P2 < $P2_required)};
     if ($P2 < $P2_required){
         push @{$self->{warn}}, ">> WARNING: -log10 probability of 2 or fewer stars < $P2_required\n";
     }
+    # If OR and P2 less than 3.0, yellow_warn.  This probably doesn't need the check on OR/ER
+    # because if it is an ER and < 3.0 the if statement above was hit.
+    elsif (($self->{obsid} < $ER_MIN_OBSID) and ($P2 < 3.0)){
+        push @{$self->{yellow_warn}}, ">> WARNING: -log10 probability of 2 or fewer stars < 3.0\n";
+    }
+
 }
 
 

From 4e289bf4d16f677e2e016e5b321acc411f3754e0 Mon Sep 17 00:00:00 2001
From: Tom Aldcroft <taldcroft@gmail.com>
Date: Thu, 17 Jan 2019 06:51:51 -0500
Subject: [PATCH 23/23] Make a consistent P2_yellow which is P2_red + 1.0

---
 starcheck/src/lib/Ska/Starcheck/Obsid.pm | 32 ++++++++++++++++--------
 starcheck/src/starcheck.pl               |  2 +-
 2 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/starcheck/src/lib/Ska/Starcheck/Obsid.pm b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
index 39b979d9..f6f40427 100644
--- a/starcheck/src/lib/Ska/Starcheck/Obsid.pm
+++ b/starcheck/src/lib/Ska/Starcheck/Obsid.pm
@@ -2823,7 +2823,7 @@ sub proseco_args{
 
 
 ###################################################################################
-sub set_proseco_probs{
+sub set_proseco_probs_and_check_P2{
 ###################################################################################
 # For observations with a star catalog and which have valid parameters already determined
 # in $self->{proseco_args}, call the Python proseco_probs method to calculate the
@@ -2851,18 +2851,28 @@ sub set_proseco_probs{
     }
     $self->{acq_probs} = \%slot_probs;
 
-    # Set the P2 requirement to be 2.0 for ORs and 3.0 for ERs.
-    my $P2_required = $self->{obsid} < $ER_MIN_OBSID ? 2.0 : 3.0;
+    # Red and yellow warnings on acquisition safing probability.
+
+    # Set the P2 requirement to be 2.0 for ORs and 3.0 for ERs.  The higher limit for ER
+    # reflects a desire to minimize integrated mission risk for observations where the
+    # attitude can be selected freely.  Yellow warning for marginal catalog is set to a
+    # factor of 10 less risk than the red limit P2 probability for OR / ER respectively).
+    my $P2_red = $self->{obsid} < $ER_MIN_OBSID ? 2.0 : 3.0;
+    my $P2_yellow = $P2_red + 1.0;
+
+    # Create a structure that gets used for report generation only.
     $self->{figure_of_merit} = {expected => substr($expected, 0, 4),
                                 P2 => $P2,
-                                cum_prob_bad => ($P2 < $P2_required)};
-    if ($P2 < $P2_required){
-        push @{$self->{warn}}, ">> WARNING: -log10 probability of 2 or fewer stars < $P2_required\n";
-    }
-    # If OR and P2 less than 3.0, yellow_warn.  This probably doesn't need the check on OR/ER
-    # because if it is an ER and < 3.0 the if statement above was hit.
-    elsif (($self->{obsid} < $ER_MIN_OBSID) and ($P2 < 3.0)){
-        push @{$self->{yellow_warn}}, ">> WARNING: -log10 probability of 2 or fewer stars < 3.0\n";
+                                cum_prob_bad => ($P2 < $P2_red)};
+
+    # Do the actual checks
+    if ($P2 < $P2_red){
+        push @{$self->{warn}},
+             ">> WARNING: -log10 probability of 2 or fewer stars < $P2_red\n";
+    }
+    elsif ($P2 < $P2_yellow){
+        push @{$self->{yellow_warn}},
+             ">> WARNING: -log10 probability of 2 or fewer stars < $P2_yellow\n";
     }
 
 }
diff --git a/starcheck/src/starcheck.pl b/starcheck/src/starcheck.pl
index 1caf3a3a..b5bd9ce6 100755
--- a/starcheck/src/starcheck.pl
+++ b/starcheck/src/starcheck.pl
@@ -637,7 +637,7 @@ sub json_obsids{
     $obs{$obsid}->check_dither($dither);
     # Get the args that proseco would want
     $obs{$obsid}->{'proseco_args'} = $obs{$obsid}->proseco_args();
-    $obs{$obsid}->set_proseco_probs();
+    $obs{$obsid}->set_proseco_probs_and_check_P2();
     $obs{$obsid}->check_star_catalog($or{$obsid}, $par{vehicle});
     $obs{$obsid}->check_sim_position(@sim_trans) unless $par{vehicle};
 	$obs{$obsid}->check_momentum_unload(\@bs);